-<H4> Update Time 10/12/14---15:03:18 </H4>
+<H4> Update Time 09/22/15---06:39:48 </H4>
<UL> <H2> Alphabetical List </H2>
<LI> <A HREF="Cluster.html"> Cluster</A>
<LI> <A HREF="Contour.html"> Contour</A>
<LI> <A HREF="Socket.html"> Socket</A>
<LI> <A HREF="SpecialNumber.html"> SpecialNumber</A>
<LI> <A HREF="String.html"> String</A>
+<LI> <A HREF="TclTk.html"> TclTk</A>
<LI> <A HREF="Vector.html"> Vector</A>
<LI> <A HREF="Vector.BACKUP.13752.html.html"> Vector.BACKUP.13752.html</A>
<LI> <A HREF="Vector.BACKUP.13830.html.html"> Vector.BACKUP.13830.html</A>
<LI> <A HREF="emData.LOCAL.14307.html.html"> emData.LOCAL.14307.html</A>
<LI> <A HREF="emData.REMOTE.14307.html.html"> emData.REMOTE.14307.html</A>
<LI> <A HREF="eosFunc.html"> eosFunc</A>
+<LI> <A HREF="eosOpenGL.html"> eosOpenGL</A>
<LI> <A HREF="eosPThread.html"> eosPThread</A>
<LI> <A HREF="eosPoint.html"> eosPoint</A>
<LI> <A HREF="gifFile.html"> gifFile</A>
/* Below Layer */
clusterLogOneRecord* belowLayerForN;
clusterLogOneRecord* belowLayerForM;
+ /* Below Layer Search Flag */
+ clusterTypeInteger alreadySearchedN;
+ clusterTypeInteger alreadySearchedM;
+ clusterTypeReal posX;
+ clusterTypeReal posY;
/* Including the below layer */
clusterTypeInteger clusterSize; /* File Number of the cluster */
extern clusterLogOneRecord* clusterLogWriteAllBinary(clusterLog* cluster, char* basename, int mode);
extern clusterLogOneRecord* clusterLogWrite(clusterLog* cluster, FILE* fpt, int mode);
+extern clusterLogOneRecord* clusterLogWriteBinary2(clusterLog* cluster, FILE* fpt, int mode);
extern clusterLogOneRecord* clusterLogWriteOneRecord(clusterLogOneRecord* cluster, FILE* fpt, int mode);
+extern clusterLogOneRecord* clusterLogWriteOneRecordBinary2(clusterLogOneRecord* cluster, FILE* fpt, int mode);
extern clusterLogOneRecord* clusterLogWriteAll(clusterLog* cluster, FILE* fpt, int mode);
+extern clusterLogOneRecord* clusterLogWriteAllBinary2(clusterLog* cluster, FILE* fpt, int mode);
extern clusterLogOneRecord* clusterLogWriteClusterOnly(clusterLog* cluster, FILE* fpt, int mode);
extern void clusterLogWritePS(clusterLog* cluster, clusterTreeInfo* linfo, FILE* fpt, int mode);
--- /dev/null
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+</PRE>
+<HR>
+<A NAME="include">
+<H2>TclTk.h</H2>
+</A>
+<PRE>
+</PRE>
long flagMolecEnvTable;
molecularEnvelope MolecEnvTable;
/* For Lorentzian */
- float flagElastic;
+ long flagElastic;
float Elastic;
float ElasticShift;
float ElasticWidth;
#define DMFILE_H
#include <stdio.h>
+#include "mrcImage.h"
/* constant begin */
typedef __int16_t dmFileInteger2;
typedef __int8_t dmFileInteger1;
+typedef enum dmFileTagDirType {
+ dmFileTagDirTypeFileEnd = 0x00,
+ dmFileTagDirTypeTagDir = 0x14,
+ dmFileTagDirTypeTag = 0x15
+} dmFileTagDirType;
+
+static char* __dmFileTagDirTypeChar[] = {
+ "FileEnd", "", "", "", "", "", "", "",
+ "", "", "", "", "", "", "", "",
+ "", "", "", "", "TagDir", "Tag"
+};
+
typedef enum dmFileTagDataType {
- dmFileTagDataTypeShort=2,
- dmFileTagDataTypeLong =3,
- dmFileTagDataTypeUShort =4,
+ dmFileTagDataTypeInt2 =2,
+ dmFileTagDataTypeInt4 =3,
+ dmFileTagDataTypeUInt2 =4,
+ dmFileTagDataTypeUInt4 =5,
+ dmFileTagDataTypeReal4 =6,
+ dmFileTagDataTypeReal8 =7,
+ dmFileTagDataTypeBool1 =8,
+ dmFileTagDataTypeChar1 =9,
+ dmFileTagDataTypeInt1 =0xa,
+ dmFileTagDataTypeInt8 =0xb,
+ dmFileTagDataTypeUInt8 =0xc,
+ dmFileTagDataTypeStruct =0xf,
+ dmFileTagDataTypeString =0x12,
+ dmFileTagDataTypeArray =0x14,
+ dmFileTagDataTypeTags =0x15,
} dmFileTagDataType;
-typedef struct dm3FileHeader {
+typedef enum dmFileImageDataType {
+ dmFileImageDataTypeInt2 = 1,
+ dmFileImageDataTypeReal4 = 2,
+ dmFileImageDataTypeComplex8 = 3,
+ dmFileImageDataTypeUnknown = 4,
+ dmFileImageDataTypePackedComplex = 5,
+ dmFileImageDataTypeUInt1 = 6,
+ dmFileImageDataTypeInt4 = 7,
+ dmFileImageDataTypeRGBInt4 = 8,
+ dmFileImageDataTypeInt1 = 9,
+ dmFileImageDataTypeUInt2 = 10,
+ dmFileImageDataTypeUInt4 = 11,
+ dmFileImageDataTypeReal8 = 12,
+ dmFileImageDataTypeComplex16= 13,
+ dmFileImageDataTypeBool1 = 14,
+ dmFileImageDataTypeIRGInt4Thumnail = 23
+} dmFileImageDataType;
+
+static size_t __dmFileImageDataTypeSize[] = {
+ 0, 2, 3, 8, 0, 4, 1, 4,
+ 4, 1, 2, 4, 6, 16, 1, 0,
+ 0, 0, 0, 0, 0, 0, 0, 4
+};
+
+static size_t __dmFileTagDataTypeSize[] = {
+ 0, 0, 2, 4, 2, 4, 4, 8,
+ 1, 1, 1, 8, 8, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0
+};
+
+/*
+static char* __dmFileTagDataTypeFormat[] = {
+ 0, 0, "%d", "%d", "%u", "%u", "%f", "%f",
+ "%d", "%c", "%d", "%lld", "%llu", 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0
+};
+*/
+
+static char* __dmFileTagDataTypeFormat[] = {
+ 0, 0, "%#0x", "%#0x", "%#0X", "%#0X", "%f", "%f",
+ "%#0x", "%c", "%#0x", "%#0x", "%#0llX", 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0
+};
+
+
+static char* __dmFileTagDataTypeChar[] = {
+ "", "", "Int2", "Int4", "UInt2", "UInt4", "Real4", "Real8",
+"Bool1", "Char1", "Int1", "Int8", "UInt8", "", "", "Struct",
+ "", "", "String", "", "Array", "Tags", "", ""
+};
+
+
+
+// Header
+typedef struct dmFile3Header {
dmFileInteger4 version;
dmFileInteger4 rootLength;
dmFileInteger4 byteOrder;
-} dm3FileHeader;
+} __attribute__((__packed__)) dmFile3Header;
-typedef struct dm4FileHeader {
+typedef struct dmFile4Header {
dmFileInteger4 version;
dmFileInteger8 rootLength;
dmFileInteger4 byteOrder;
-} dm4FileHeader;
+} __attribute__((__packed__)) dmFile4Header;
+
+typedef struct dmFile3TagDirectory dmFile3TagDirectory;
+typedef struct dmFile4TagDirectory dmFile4TagDirectory;
-typedef struct dm3FileTagDirectrory {
+// Tag
+typedef struct dmFile3Tag {
dmFileInteger1 tagID;
dmFileInteger2 tagNameLength; // Bytes
char* tagName;
- dmFileInteger8 tagDataSize; // Bytes
-} dm3FileTagDirectrory;
+ // Tag
+ char seperator[4];
+ dmFileInteger4 ninfo;
+ dmFileInteger4* info;
+ long pValue; // Offset
+ void* value; // Array or value
+ void** value2; // Struct
+ void** value3; // Array of Struct
+ // TagDirectory
+ dmFile3TagDirectory* tagDir;
+} dmFile3Tag;
-typedef struct dm4FileTagDirectrory {
+typedef struct dmFile4Tag {
dmFileInteger1 tagID;
dmFileInteger2 tagNameLength; // Bytes
char* tagName;
- dmFileInteger8 tagDataSize; // Bytes
-} dm4FileTagDirectrory;
+ dmFileInteger8 tagLength;
+ // Tag
+ char seperator[4];
+ dmFileInteger8 ninfo;
+ dmFileInteger8* info;
+ long pValue;
+ void* value; // Array or value
+ void** value2; // Struct
+ void** value3; // Array of Struct
+ // TagDirectory
+ dmFile4TagDirectory* tagDir;
+} dmFile4Tag;
-typedef struct dm3FileRootTagDirectory {
+// Root Tag Directory
+struct dmFile3TagDirectory {
dmFileInteger1 sortf;
dmFileInteger1 closef;
dmFileInteger4 numberOfTags;
-} dm3FileRootTagDirectory;
+ dmFile3Tag* Tags;
+} ;
-typedef struct dm4FileRootTagDirectory {
+struct dmFile4TagDirectory {
dmFileInteger1 sortf;
dmFileInteger1 closef;
dmFileInteger8 numberOfTags;
-} dm4FileRootTagDirectory;
+ dmFile4Tag* Tags;
+} ;
typedef struct dmFile {
// Header
dmFileInteger4 version;
- dm3FileHeader Header3;
- dm4FileHeader Header4;
+ dmFile3Header Header3;
+ dmFile4Header Header4;
// Root Tag
- dm3FileRootTagDirectory RootTag3;
- dm4FileRootTagDirectory RootTag4;
-
+ dmFile3TagDirectory RootTag3;
+ dmFile4TagDirectory RootTag4;
+ // Tail
dmFileInteger8 Tail;
+
+ //
+ mrcImage thumnail;
+ mrcImage image;
} dmFile;
/* struct end */
// in dfFileInfo.c
extern void dmFileInfo(FILE* fpt, dmFile dm, int mode);
+extern void dmFileHeaderInfo(FILE* fpt, dmFile dm, int mode);
+extern void dmFile3TagDirectoryInfo(FILE* fpt, dmFile3TagDirectory tagDir, int layer, int mode);
+extern void dmFile3TagInfo(FILE* fpt, dmFile3Tag tagr, int layer, int mode);
+extern void dmFile4TagDirectoryInfo(FILE* fpt, dmFile4TagDirectory tagDir, int layer, int mode);
+extern void dmFile4TagInfo(FILE* fpt, dmFile4Tag tag, int layer, int mode);
// in dmFileRead.c
extern void dmFileRead(FILE* fpt, dmFile* dm, char* message, int mode);
+// DM Header and End Read: check file format
+extern void dmFileHeaderTailRead(FILE* fpt, dmFile* dm, char* message, int mode);
+// DM3
+// Header
+extern void dmFile3HeaderRead(FILE* fpt, dmFile* dm, char* message, int mode);
+//
+extern void dmFile3TagDirectoryHeaderRead(FILE* fpt, dmFile3TagDirectory* dmRoot, char* message, int mode);
+extern void dmFile3TagHeaderRead(FILE* fpt, dmFile3Tag* dmTag, char* message, int mode);
+extern void dmFile3TagRead(FILE* fpt, dmFile3Tag* dmTag, char* message, int mode);
+extern void dmFile3TagDirectoryRead(FILE* fpt, dmFile3TagDirectory* dmTagDir, char* message, int mode);
+
+// DM4
+// Header
+extern void dmFile4HeaderRead(FILE* fpt, dmFile* dm, char* message, int mode);
+//
+extern void dmFile4TagDirectoryHeaderRead(FILE* fpt, dmFile4TagDirectory* dmRoot, char* message, int mode);
+extern void dmFile4TagHeaderRead(FILE* fpt, dmFile4Tag* dmTag, char* message, int mode);
+extern void dmFile4TagRead(FILE* fpt, dmFile4Tag* dmTag, char* message, int mode);
+extern void dmFile4TagDirectoryRead(FILE* fpt, dmFile4TagDirectory* dmTagDir, char* message, int mode);
+
+// in dmFileUtil.c
+extern void dmFileValuePrint(FILE* fpt, void* value, dmFileTagDataType valueType, int n);
+
+// in dm2mrc.c
+extern void ldm2mrc(mrcImage* mrc, dmFile* dm, int mode);
+extern void dmFile3TagDirectory2mrc(dmFile* fpt, dmFile3TagDirectory tagDir, int layer, int mode);
+extern void dmFile4TagDirectory2mrc(dmFile* fpt, dmFile4TagDirectory tagDir, int layer, int mode);
+// in dmFileInit.c
+extern void dmFileInit(dmFile* dm, int mode);
/* prototype end */
--- /dev/null
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+</PRE>
+<HR>
+<A NAME="include">
+<H2>eosOpenGL.h</H2>
+</A>
+<PRE>
+#ifndef EOS_OPENGL
+#define EOS_OPENGL
+
+#ifdef X86MAC64
+#include <GLUT/glut.h>
+#else
+#include <GL/glut.h>
+#endif
+
+extern void __openGLAA(void);
+extern void openGLKeyDefault(char c, int x, int y );
+#endif /* EOS_OPENGL */
+</PRE>
long flagrmax;
double RMS; /* Root mean square */
int mode;
+ mrcImageParaTypeRealCoord sdOfAllAxis;
+ mrcImageParaTypeRealCoord aveOfAllAxis;
/* For Search Area */
int flagXrange;
meanOfCentre = 4,
meanOfSparse = 5,
meanOf2DEdgeY = 6,
- RMSofAllPixels = 7
+ RMSofAllPixels = 7,
+ sdOfAllAxis = 8
} mrcImageInformationMode;
/*
extern void lmrcImageCorrelation(mrcImage* out, mrcImage* in, mrcImage* ref, long mode);
extern void lmrcImageCorrelationModePrint(FILE* fpt);
+/* in lMrcImagePattersonFunctionCalc.c */
+extern void lmrcImagePattersonFunctionCalc(mrcImage* out, mrcImage* in);
+extern void lmrcImagePattersonFunctionPrint(FILE* fpt, mrcImage* in, int mode);
+
#include "ctfInfo.h"
extern void lmrcImageCorrelationWithCTFCompensation(mrcImage* out, mrcImage* in, ctfInfo* inctf, mrcImage* ref, ctfInfo* refctf, long mode);
<LI> <A HREF="anglediffcalc.html"> anglediffcalc</A>
<LI> <A HREF="anglediffchk.html"> anglediffchk</A>
<LI> <A HREF="array2mrc.html"> array2mrc</A>
+<LI> <A HREF="arrayPCA.html"> arrayPCA</A>
<LI> <A HREF="bin2mrc.html"> bin2mrc</A>
<LI> <A HREF="bmp2mrc.html"> bmp2mrc</A>
<LI> <A HREF="bmpFileInfo.html"> bmpFileInfo</A>
<LI> <A HREF="ctfDetermine.html"> ctfDetermine</A>
<LI> <A HREF="ctfDisplay.html"> ctfDisplay</A>
<LI> <A HREF="ctfEnvelopFunction.html"> ctfEnvelopFunction</A>
+<LI> <A HREF="ctfEnvelopFunctionEstimate.html"> ctfEnvelopFunctionEstimate</A>
<LI> <A HREF="ctfFunction.html"> ctfFunction</A>
<LI> <A HREF="ctfFunctionServer.html"> ctfFunctionServer</A>
<LI> <A HREF="ctfInfoSet.html"> ctfInfoSet</A>
<LI> <A HREF="dcdTest.html"> dcdTest</A>
<LI> <A HREF="dcdTimeSeriesBehavior.html"> dcdTimeSeriesBehavior</A>
<LI> <A HREF="defocusDeterminationFromThonRing.html"> defocusDeterminationFromThonRing</A>
+<LI> <A HREF="dm2mrc.html"> dm2mrc</A>
<LI> <A HREF="dmInfo.html"> dmInfo</A>
<LI> <A HREF="dos2unix.html"> dos2unix</A>
<LI> <A HREF="electronWaveLength.html"> electronWaveLength</A>
<LI> <A HREF="emData2mrc.html"> emData2mrc</A>
<LI> <A HREF="energyTransferModelCheck.html"> energyTransferModelCheck</A>
<LI> <A HREF="energyTransferModelResultCheck.html"> energyTransferModelResultCheck</A>
+<LI> <A HREF="eosBayesInit.html"> eosBayesInit</A>
<LI> <A HREF="eosPointProjector.html"> eosPointProjector</A>
<LI> <A HREF="eosPointRotation.html"> eosPointRotation</A>
<LI> <A HREF="eosPointTracker.html"> eosPointTracker</A>
<LI> <A HREF="mrcImage3DHighResoEmphasis.html"> mrcImage3DHighResoEmphasis</A>
<LI> <A HREF="mrcImage3DPad.html"> mrcImage3DPad</A>
<LI> <A HREF="mrcImage3DPad2.html"> mrcImage3DPad2</A>
+<LI> <A HREF="mrcImage3DPeakGet.html"> mrcImage3DPeakGet</A>
<LI> <A HREF="mrcImage3DSymmetryFind.html"> mrcImage3DSymmetryFind</A>
<LI> <A HREF="mrcImage3DWindowing.html"> mrcImage3DWindowing</A>
<LI> <A HREF="mrcImageAbnormalValueRemove.html"> mrcImageAbnormalValueRemove</A>
<LI> <A HREF="mrcImageAutoRotationCorrelation.html"> mrcImageAutoRotationCorrelation</A>
<LI> <A HREF="mrcImageAutoRotationCorrelation3D.html"> mrcImageAutoRotationCorrelation3D</A>
<LI> <A HREF="mrcImageAutoRotationCorrelationResultPrint.html"> mrcImageAutoRotationCorrelationResultPrint</A>
+<LI> <A HREF="mrcImageAutoTriming.html"> mrcImageAutoTriming</A>
<LI> <A HREF="mrcImageAverage.html"> mrcImageAverage</A>
<LI> <A HREF="mrcImageBandPassFilter.html"> mrcImageBandPassFilter</A>
<LI> <A HREF="mrcImageBilateralFilter.html"> mrcImageBilateralFilter</A>
<LI> <A HREF="mrcImageCenterDensityChange.html"> mrcImageCenterDensityChange</A>
<LI> <A HREF="mrcImageCenterGet.html"> mrcImageCenterGet</A>
<LI> <A HREF="mrcImageCenterOfMassCalculate.html"> mrcImageCenterOfMassCalculate</A>
+<LI> <A HREF="mrcImageChainCodeCalc.html"> mrcImageChainCodeCalc</A>
<LI> <A HREF="mrcImageCircumferentialProjection.html"> mrcImageCircumferentialProjection</A>
<LI> <A HREF="mrcImageClosing.html"> mrcImageClosing</A>
<LI> <A HREF="mrcImageClusterAnalysis.html"> mrcImageClusterAnalysis</A>
<LI> <A HREF="mrcImageDivideInfoForTomography.html"> mrcImageDivideInfoForTomography</A>
<LI> <A HREF="mrcImageDivideIntoTwoImages.html"> mrcImageDivideIntoTwoImages</A>
<LI> <A HREF="mrcImageDividedByFile.html"> mrcImageDividedByFile</A>
+<LI> <A HREF="mrcImageEdgeCalc.html"> mrcImageEdgeCalc</A>
<LI> <A HREF="mrcImageEdgeEnhancement.html"> mrcImageEdgeEnhancement</A>
<LI> <A HREF="mrcImageEdgeImageGet.html"> mrcImageEdgeImageGet</A>
<LI> <A HREF="mrcImageEnhancementWithFuzzySets.html"> mrcImageEnhancementWithFuzzySets</A>
<LI> <A HREF="mrcImageExpression.html"> mrcImageExpression</A>
<LI> <A HREF="mrcImageFFT.html"> mrcImageFFT</A>
<LI> <A HREF="mrcImageFFTLayerLineExtraction.html"> mrcImageFFTLayerLineExtraction</A>
+<LI> <A HREF="mrcImageFFTSetsExtract.html"> mrcImageFFTSetsExtract</A>
<LI> <A HREF="mrcImageFOMCalc.html"> mrcImageFOMCalc</A>
<LI> <A HREF="mrcImageFTest.html"> mrcImageFTest</A>
+<LI> <A HREF="mrcImageFeatureCalc.html"> mrcImageFeatureCalc</A>
<LI> <A HREF="mrcImageFeatureExtraction.html"> mrcImageFeatureExtraction</A>
<LI> <A HREF="mrcImageFilamentSearch.html"> mrcImageFilamentSearch</A>
<LI> <A HREF="mrcImageFilterCreate.html"> mrcImageFilterCreate</A>
<LI> <A HREF="mrcImageHelicalProjection.html"> mrcImageHelicalProjection</A>
<LI> <A HREF="mrcImageHighPassFilter.html"> mrcImageHighPassFilter</A>
<LI> <A HREF="mrcImageHighlighting.html"> mrcImageHighlighting</A>
+<LI> <A HREF="mrcImageHoughTransform.html"> mrcImageHoughTransform</A>
+<LI> <A HREF="mrcImageHoughTransformInverse.html"> mrcImageHoughTransformInverse</A>
<LI> <A HREF="mrcImageInfo.html"> mrcImageInfo</A>
<LI> <A HREF="mrcImageInverseRadonTransform.html"> mrcImageInverseRadonTransform</A>
<LI> <A HREF="mrcImageLabeling.html"> mrcImageLabeling</A>
+<LI> <A HREF="mrcImageLocalMaximumValuesFind.html"> mrcImageLocalMaximumValuesFind</A>
<LI> <A HREF="mrcImageLogicalOperation.html"> mrcImageLogicalOperation</A>
<LI> <A HREF="mrcImageLowPassFilter.html"> mrcImageLowPassFilter</A>
<LI> <A HREF="mrcImageMagnificationChange.html"> mrcImageMagnificationChange</A>
<LI> <A HREF="mrcImageMappingtoPdb.html"> mrcImageMappingtoPdb</A>
<LI> <A HREF="mrcImageMasking.html"> mrcImageMasking</A>
<LI> <A HREF="mrcImageMaskingByImage.html"> mrcImageMaskingByImage</A>
+<LI> <A HREF="mrcImageMeanFreePathCalc.html"> mrcImageMeanFreePathCalc</A>
<LI> <A HREF="mrcImageMergebyside.html"> mrcImageMergebyside</A>
<LI> <A HREF="mrcImageMirroring.html"> mrcImageMirroring</A>
<LI> <A HREF="mrcImageModeChange.html"> mrcImageModeChange</A>
<LI> <A HREF="mrcImagePad.html"> mrcImagePad</A>
<LI> <A HREF="mrcImagePanoramaCreate.html"> mrcImagePanoramaCreate</A>
<LI> <A HREF="mrcImageParticleCandidateExtract.html"> mrcImageParticleCandidateExtract</A>
+<LI> <A HREF="mrcImagePattersonFunctionCalc.html"> mrcImagePattersonFunctionCalc</A>
<LI> <A HREF="mrcImagePeakSearch.html"> mrcImagePeakSearch</A>
+<LI> <A HREF="mrcImagePerimeterCalc.html"> mrcImagePerimeterCalc</A>
<LI> <A HREF="mrcImagePhaseCTFCompensationFromCTFINFO.html"> mrcImagePhaseCTFCompensationFromCTFINFO</A>
<LI> <A HREF="mrcImagePixelDataGet.html"> mrcImagePixelDataGet</A>
<LI> <A HREF="mrcImagePolyROI.html"> mrcImagePolyROI</A>
<LI> <A HREF="mrcImageRotation.html"> mrcImageRotation</A>
<LI> <A HREF="mrcImageRotation3D.html"> mrcImageRotation3D</A>
<LI> <A HREF="mrcImageSN.html"> mrcImageSN</A>
+<LI> <A HREF="mrcImageSNEstimate.html"> mrcImageSNEstimate</A>
<LI> <A HREF="mrcImageSamplingUnitChange.html"> mrcImageSamplingUnitChange</A>
<LI> <A HREF="mrcImageScalarAdd.html"> mrcImageScalarAdd</A>
<LI> <A HREF="mrcImageSectionGet.html"> mrcImageSectionGet</A>
<LI> <A HREF="mrcImageShapeOrientation.html"> mrcImageShapeOrientation</A>
<LI> <A HREF="mrcImageShapePCA.html"> mrcImageShapePCA</A>
<LI> <A HREF="mrcImageShapePCAFit.html"> mrcImageShapePCAFit</A>
+<LI> <A HREF="mrcImageShapeSearch.html"> mrcImageShapeSearch</A>
<LI> <A HREF="mrcImageShift.html"> mrcImageShift</A>
<LI> <A HREF="mrcImageShiftFollowingGC.html"> mrcImageShiftFollowingGC</A>
<LI> <A HREF="mrcImageShrink.html"> mrcImageShrink</A>
<LI> <A HREF="mrcImageSubstraction.html"> mrcImageSubstraction</A>
<LI> <A HREF="mrcImageSubtraction.html"> mrcImageSubtraction</A>
<LI> <A HREF="mrcImageSuperResolution.html"> mrcImageSuperResolution</A>
+<LI> <A HREF="mrcImageSurfaceAreaCalc.html"> mrcImageSurfaceAreaCalc</A>
+<LI> <A HREF="mrcImageSurfaceCalc.html"> mrcImageSurfaceCalc</A>
<LI> <A HREF="mrcImageSymmetryAverage.html"> mrcImageSymmetryAverage</A>
<LI> <A HREF="mrcImageSymmetryCentreFind.html"> mrcImageSymmetryCentreFind</A>
<LI> <A HREF="mrcImageSymmetryFind.html"> mrcImageSymmetryFind</A>
<LI> <A HREF="mrcImageTiltAxisSearchHelp.html"> mrcImageTiltAxisSearchHelp</A>
<LI> <A HREF="mrcImageToNAMDConstantForces.html"> mrcImageToNAMDConstantForces</A>
<LI> <A HREF="mrcImageToPointsSet.html"> mrcImageToPointsSet</A>
+<LI> <A HREF="mrcImageToneReversal.html"> mrcImageToneReversal</A>
<LI> <A HREF="mrcImageTopHatTransform.html"> mrcImageTopHatTransform</A>
<LI> <A HREF="mrcImageTrans.html"> mrcImageTrans</A>
<LI> <A HREF="mrcImageTransepose.html"> mrcImageTransepose</A>
<LI> <A HREF="mrcImageTwoImageTest.html"> mrcImageTwoImageTest</A>
<LI> <A HREF="mrcImageUnbentROI.html"> mrcImageUnbentROI</A>
<LI> <A HREF="mrcImageUnexpectedMassFromPDB.html"> mrcImageUnexpectedMassFromPDB</A>
+<LI> <A HREF="mrcImageUnsharpening.html"> mrcImageUnsharpening</A>
<LI> <A HREF="mrcImageUntwist.html"> mrcImageUntwist</A>
<LI> <A HREF="mrcImageVarianceAnalysis.html"> mrcImageVarianceAnalysis</A>
<LI> <A HREF="mrcImageVarianceMap.html"> mrcImageVarianceMap</A>
<LI> <A HREF="pgSelect.html"> pgSelect</A>
<LI> <A HREF="pointAffineTransform.html"> pointAffineTransform</A>
<LI> <A HREF="pointsSetToPDB.html"> pointsSetToPDB</A>
+<LI> <A HREF="probabilityDensityFunction.html"> probabilityDensityFunction</A>
<LI> <A HREF="psFileMerge.html"> psFileMerge</A>
<LI> <A HREF="psFilePageMerge.html"> psFilePageMerge</A>
<LI> <A HREF="randomNormalGet.html"> randomNormalGet</A>
<PRE>
Usage: CheckCommonLineData
Options:
- [-I[nput] In (NULL )] :Essential :InputDataFileList
- [-o[utput]R[eal] OutR (NULL )] :Essential :OutputDataFile
- [-o[utput]I[m] OutI (NULL )] :Essential :OutputDataFile
- [-o[utput]L[ength] OutL (NULL )] :Essential :OutputDataFile
- [-o[utput]P[hase] OutP (NULL )] :Essential :OutputDataFile
- [-o[utput]LL OutLL (NULL )] :Essential :OutputDataFile
- [-Log Log (NULL )] :Essential :LogFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-I[nput] In (NULL ).as(inFileListNoOpen ) ] :Essential :InputDataFileList
+ [-o[utput]R[eal] OutR (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-o[utput]I[m] OutI (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-o[utput]L[ength] OutL (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-o[utput]P[hase] OutP (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-o[utput]LL OutLL (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-Log Log (NULL ).as(outFile ) ] :Essential :LogFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: CheckOfOrientation
Options:
- [-I[nputFileList] InList (NULL )] :Essential :InputDataFileList
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-o[utput]v[alue] OutV (NULL )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-I[nputFileList] InList (NULL ).as(inFileListNoOpen ) ] :Essential :InputDataFileList
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-o[utput]v[alue] OutV (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----------- Output file -------------
-o : output Matrix data
<PRE>
Usage: CommonLineCalculation
Options:
- [-i[nput] In (NULL )] :Optional :InputDataFile
- [-I[nputfilelist] InList (NULL )] :Optional :InputDatalistFile
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (1 )] :Optional :Mode
- [-I[nput]m[ode] Inputmode (0 )] :Optional :InputMode
+ [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputDataFile
+ [-I[nputfilelist] InList (NULL ).as(inFileListNoOpen ) ] :Optional :InputDatalistFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (1 ).as(Integer ) ] :Optional :Mode
+ [-I[nput]m[ode] Inputmode (0 ).as(Integer ) ] :Optional :InputMode
----- mode -----
-m : 0 : in 2004/07/22
<PRE>
Usage: Descartes2Polar
Options:
- [-i x (0.0 )y (1.0 )z (0.0 )] :Optional :input: coord
- [-o Out (stdout )] :Optional :output: coord
- [-centre cx (0.0 )cy (0.0 )cz (0.0 )] :Optional :Centre
- [-xaxis xx (1.0 )xy (0.0 )xz (0.0 )] :Optional :x-axis
- [-zaxis zx (0.0 )zy (0.0 )zz (1.0 )] :Optional :z-axis
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i x (0.0 ).as(Real )
+ y (1.0 ).as(Real )
+ z (0.0 ).as(Real ) ] :Optional :input: coord
+ [-o Out (stdout ).as(outFile ) ] :Optional :output: coord
+ [-centre cx (0.0 ).as(Real )
+ cy (0.0 ).as(Real )
+ cz (0.0 ).as(Real ) ] :Optional :Centre
+ [-xaxis xx (1.0 ).as(Real )
+ xy (0.0 ).as(Real )
+ xz (0.0 ).as(Real ) ] :Optional :x-axis
+ [-zaxis zx (0.0 ).as(Real )
+ zy (0.0 ).as(Real )
+ zz (1.0 ).as(Real ) ] :Optional :z-axis
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: Display2
Options:
- [-i[nput] In (NULL )] :Optional :InputDataFile
- [-t[epmlate] Template (2056251152.roi )] :Optional :Template for InputFile
- [-H[ighForThres] ThresHigh (0.0 )] :Optional :Template for InputFile
- [-L[owForThres] ThresLow (0.0 )] :Optional :Template for InputFile
- [-Zoom Zoom (1.0 )] :Optional :Zoom for InputFile
- [-Inverse ] :Optional :Inverse (HighValue(dark)<->LowValue(bright)) for InputFile
- [-o[utput] Out (.EosLog )] :Optional :OutputLogFile
- [-display geometry (:0.0 )] :Optional :OutputLogFile
- [-geometry display (1024x1024+0+0)] :Optional :OutputLogFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputDataFile
+ [-t[epmlate] Template (%d.roi ).as(String ) ] :Optional :Template for InputFile
+ [-H[ighForThres] ThresHigh (0.0 ).as(Real ) ] :Optional :Template for InputFile
+ [-L[owForThres] ThresLow (0.0 ).as(Real ) ] :Optional :Template for InputFile
+ [-Zoom Zoom (1.0 ).as(Real ) ] :Optional :Zoom for InputFile
+ [-Inverse ] :Optional :Inverse (HighValue(dark)<->LowValue(bright)) for InputFile
+ [-o[utput] Out (.EosLog ).as(String ) ] :Optional :OutputLogFile
+ [-display geometry (:0.0 ).as(String ) ] :Optional :OutputLogFile
+ [-geometry display (1024x1024+0+0).as(String ) ] :Optional :OutputLogFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
New wish commands of Display2
mrcInfoSet [z|min|max] value
mrcInfoSet [log|pow]
<PRE>
Usage: EvaluateCorrelationMapwithCommonLine
Options:
- [-i[nput] In (NULL )] :Essential :InputCorrelationMapList
- [-i[nput]c[ommonLine]InC (NULL )] :Essential :InputCommonLineDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-P[eakArea]M[ode] Pm (0 )] :Optional :PeakDetectAreaMode
- [-P[eak]N[umber] PN (10 )] :Optional :PeakNumber
- [-PDT[hres] PDT (0.2 )] :Optional :PeakDetectThreshold_ForMode0
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputCorrelationMapList
+ [-i[nput]c[ommonLine]InC (NULL ).as(inFile ) ] :Essential :InputCommonLineDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-P[eakArea]M[ode] Pm (0 ).as(Integer ) ] :Optional :PeakDetectAreaMode
+ [-P[eak]N[umber] PN (10 ).as(Integer ) ] :Optional :PeakNumber
+ [-PDT[hres] PDT (0.2 ).as(Real ) ] :Optional :PeakDetectThreshold_ForMode0
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: FETOrientationSearchByAnnealing
Options:
- [-i[nputMS] InMS (NULL )] :Essential :InputMapSet
- [-i[nput]F[ile] InFL (NULL )] :Optional :InputFETDataFileList
- [-i[nput]M[aps] InML (NULL )] :Optional :InputMapDataFileList
- [-T[emprature] ITemp (300.0 )] :Optional :InitialTemprature
- [-a[nnealing]s[chedule]1AS1 (10 )] :Optional :Repeatas1TimesInSameTemp
- [-a[nnealing]s[chedule]2AS2 (0.9 )] :Optional :TempratureDecreaseConstant
- [-a[nnealing]s[chedule]3AS3 (10 )] :Optional :Repeatas3Times
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nputMS] InMS (NULL ).as(inFile ) ] :Essential :InputMapSet
+ [-i[nput]F[ile] InFL (NULL ).as(inFile ) ] :Optional :InputFETDataFileList
+ [-i[nput]M[aps] InML (NULL ).as(inFile ) ] :Optional :InputMapDataFileList
+ [-T[emprature] ITemp (300.0 ).as(Real ) ] :Optional :InitialTemprature
+ [-a[nnealing]s[chedule]1AS1 (10 ).as(Integer ) ] :Optional :Repeatas1TimesInSameTemp
+ [-a[nnealing]s[chedule]2AS2 (0.9 ).as(Real ) ] :Optional :TempratureDecreaseConstant
+ [-a[nnealing]s[chedule]3AS3 (10 ).as(Integer ) ] :Optional :Repeatas3Times
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
this tool does not work at Oct.31,2007
<PRE>
Usage: FETOrientationSearchByFeatureAlignment
Options:
- [-i[nput] InS (NULL )] :Optional :InputSinogramList
- [-i[nput]2 InS2 (NULL )] :Optional :InputMoreSinogramList
- [-I[nputFET] InF (NULL )] :Optional :InputFETfileList
- [-i[nput]a[ngle] InA (NULL )] :Optional :inputAngleList
- [-o[utput] Out (NULL )] :Optional :OutputDataFile
- [-o[ut]clog OutLOG (NULL )] :Optional :OutputCorValueLogFile
- [-o[ut]a[ngle] OutA (NULL )] :Optional :OutputAngleList
- [-o[ut]2d Out2D (NULL )] :Optional :OutputAngleListFormrc3Dto2D
- [-itm[ax] ITMAX (8 )] :Optional :iterationMax
- [-dvm[ax] DEVMAX (3 )] :Optional :sphereDevideMax
- [-mitm[ax] MITMAX (3 )] :Optional :iterationMax Multiple
- [-mdvm[ax] MDEVMAX (3 )] :Optional :sphereDevideMax Multiple
- [-ldn[um] LDN (8 )] :Optional :LongaxisDevideNum
- [-srl[imit] SRL (0.0 )] :Optional :sphereReconstLimit
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (202 )] :Optional :Mode
+ [-i[nput] InS (NULL ).as(inFile ) ] :Optional :InputSinogramList
+ [-i[nput]2 InS2 (NULL ).as(inFile ) ] :Optional :InputMoreSinogramList
+ [-I[nputFET] InF (NULL ).as(inFile ) ] :Optional :InputFETfileList
+ [-i[nput]a[ngle] InA (NULL ).as(inFile ) ] :Optional :inputAngleList
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-o[ut]clog OutLOG (NULL ).as(outFile ) ] :Optional :OutputCorValueLogFile
+ [-o[ut]a[ngle] OutA (NULL ).as(outFile ) ] :Optional :OutputAngleList
+ [-o[ut]2d Out2D (NULL ).as(outFile ) ] :Optional :OutputAngleListFormrc3Dto2D
+ [-itm[ax] ITMAX (8 ).as(Integer ) ] :Optional :iterationMax
+ [-dvm[ax] DEVMAX (3 ).as(Integer ) ] :Optional :sphereDevideMax
+ [-mitm[ax] MITMAX (3 ).as(Integer ) ] :Optional :iterationMax Multiple
+ [-mdvm[ax] MDEVMAX (3 ).as(Integer ) ] :Optional :sphereDevideMax Multiple
+ [-ldn[um] LDN (8 ).as(Integer ) ] :Optional :LongaxisDevideNum
+ [-srl[imit] SRL (0.0 ).as(Real ) ] :Optional :sphereReconstLimit
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (202 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
Either -i or -I is essential option.
Input FETimages: smoothed image is recommend.
<PRE>
Usage: FETmapOrientationSearchBySimultaneousFitting
Options:
- [-i[nput] InML (NULL )] :Essential :InputMapList
- [-i[nput]n[ame] InNL (NULL )] :Essential :InputNameList
- [-i[nput]C[ore]L[ist]InCL (NULL )] :Essential :InputCandidateCoreList
- [-P[eakArea]M[ode] PM (0 )] :Optional :PeakDetectAreaMode
- [-P[eak]N[umber] PN (10 )] :Optional :PeakNumber
- [-PDT[hres] PDT (0.2 )] :Optional :PeakDetectThreshold_ForMode0
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] InML (NULL ).as(inFile ) ] :Essential :InputMapList
+ [-i[nput]n[ame] InNL (NULL ).as(inFile ) ] :Essential :InputNameList
+ [-i[nput]C[ore]L[ist]InCL (NULL ).as(inFile ) ] :Essential :InputCandidateCoreList
+ [-P[eakArea]M[ode] PM (0 ).as(Integer ) ] :Optional :PeakDetectAreaMode
+ [-P[eak]N[umber] PN (10 ).as(Integer ) ] :Optional :PeakNumber
+ [-PDT[hres] PDT (0.2 ).as(Real ) ] :Optional :PeakDetectThreshold_ForMode0
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
InputMapList: FETcorrelationMapList
InputNameList: FETfileNameList
<PRE>
Usage: FETsmallMapSetCreate_forSimultaneousMinimization
Options:
- [-i[nput]M[ap]L[ist] InML (NULL )] :Essential :InputMapList
- [-o[utputMapSet] OutMS (NULL )] :Essential :OutputMapSet
- [-s[tep]s[ize] InSS (5 )] :Optional :StepSize
- [-s[earch]r[adius] InSR (15 )] :Optional :searchRadius-degree
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput]M[ap]L[ist] InML (NULL ).as(inFile ) ] :Essential :InputMapList
+ [-o[utputMapSet] OutMS (NULL ).as(outFile ) ] :Essential :OutputMapSet
+ [-s[tep]s[ize] InSS (5 ).as(Integer ) ] :Optional :StepSize
+ [-s[earch]r[adius] InSR (15 ).as(Integer ) ] :Optional :searchRadius-degree
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
input MapList must not have empty line.
360 % (ss*2) = 0
<PRE>
Usage: LCalculationForOrientationSearch
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: Polar2Descartes
Options:
- [-i r (1.0 )phi (90.0 )theta (0.0 )] :Optional :input: coord
- [-o Out (stdout )] :Optional :output: coord
- [-centre cx (0.0 )cy (0.0 )cz (0.0 )] :Optional :Centre
- [-xaxis xx (1.0 )xy (0.0 )xz (0.0 )] :Optional :x-axis
- [-zaxis zx (0.0 )zy (0.0 )zz (1.0 )] :Optional :z-axis
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i r (1.0 ).as(Real )
+ phi (90.0 ).as(Real )
+ theta (0.0 ).as(Real ) ] :Optional :input: coord
+ [-o Out (stdout ).as(outFile ) ] :Optional :output: coord
+ [-centre cx (0.0 ).as(Real )
+ cy (0.0 ).as(Real )
+ cz (0.0 ).as(Real ) ] :Optional :Centre
+ [-xaxis xx (1.0 ).as(Real )
+ xy (0.0 ).as(Real )
+ xz (0.0 ).as(Real ) ] :Optional :x-axis
+ [-zaxis zx (0.0 ).as(Real )
+ zy (0.0 ).as(Real )
+ zz (1.0 ).as(Real ) ] :Optional :z-axis
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: ProjectionDirectionMapCreate
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Optional :OutputDataFile
- [-p[ost]s[cript] Ps (NULL )] :Optional :OutputPostScriptFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-R[otation]m[ode] Rmode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-p[ost]s[cript] Ps (NULL ).as(outFile ) ] :Optional :OutputPostScriptFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-R[otation]m[ode] Rmode (0 ).as(Integer ) ] :Optional :Mode
----- Rotational Mode -----
Final rotation of projection is only Z .
<PRE>
Usage: WeightCalculationOfCommonLineSearch
Options:
- [-I[nput] In (NULL )] :Essential :InputDataFileList
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-L[ength]T[hreshold]M[ode]LengthThresholdMode (0 )] :Essential :Length threshold mode in LengthCorrelation
- [-L[ength]T[hreshold]R[atio]LengthThresholdRatio(0.25 )] :Optional :Length threshold ratio in LengthCorrelation : -LTM=0
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-I[nput] In (NULL ).as(inFileList ) ] :Essential :InputDataFileList
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-L[ength]T[hreshold]M[ode]LengthThresholdMode (0 ).as(Integer ) ] :Essential :Length threshold mode in LengthCorrelation
+ [-L[ength]T[hreshold]R[atio]LengthThresholdRatio(0.25 ).as(Real ) ] :Optional :Length threshold ratio in LengthCorrelation : -LTM=0
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Mode -----
-m :
<PRE>
Usage: WeightCalculationOfCommonLineSearchByAllSinogram
Options:
- [-I[nput]1 In1 (NULL )] :Optional :InputDataFileList1 : normal correlation
- [-I[nput]2 In2 (NULL )] :Optional :InputDataFileList2 : derivation1D correlation
- [-I[nput]3 In3 (NULL )] :Optional :InputDataFileList3 : derivation2D correlation
- [-I[nput]4 In4 (NULL )] :Optional :InputDataFileList4 : length correlation
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-M[ode] Mode (15 )] :Optional :Mode : choice of used Correlation
- [-v[ariance] variance (5 )] :Optional :variance of Gaussian weight function
+ [-I[nput]1 In1 (NULL ).as(inFileListNoOpen ) ] :Optional :InputDataFileList1 : normal correlation
+ [-I[nput]2 In2 (NULL ).as(inFileListNoOpen ) ] :Optional :InputDataFileList2 : derivation1D correlation
+ [-I[nput]3 In3 (NULL ).as(inFileListNoOpen ) ] :Optional :InputDataFileList3 : derivation2D correlation
+ [-I[nput]4 In4 (NULL ).as(inFileListNoOpen ) ] :Optional :InputDataFileList4 : length correlation
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-M[ode] Mode (15 ).as(Integer ) ] :Optional :Mode : choice of used Correlation
+ [-v[ariance] variance (5 ).as(Real ) ] :Optional :variance of Gaussian weight function
----- Mode -----
-M : 1 : ued to Normal Correlation
-/bin/bash: anglediffchk: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>anglediffchk</TITLE>
+</HEAD>
+<BODY>
+<H1>anglediffchk</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: anglediffchk
+Options:
+ [-t[estAngle] Test (0.0 ).as(Real ) ] :Essential :test
+ [-r[eferenceAngle] Reference (0.0 ).as(Real ) ] :Essential :reference
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :configFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: array2mrc
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-m[ode]m[rcimage] mm (2 )] :Optional :Mode of mrcImage
- [-l[ength]m[rcimage] lm (0 )] :Optional :Length of mrcImage
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-m[ode]m[rcimage] mm (2 ).as(Integer ) ] :Optional :Mode of mrcImage
+ [-l[ength]m[rcimage] lm (0 ).as(Real ) ] :Optional :Length of mrcImage
----- Additional Usage -----
-- Attension --
Array format : left-hand
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>arrayPCA</TITLE>
+</HEAD>
+<BODY>
+<H1>arrayPCA</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: arrayPCA
+Options:
+ [-i[nput] In (stdin ).as(inFile::ASCII ) ] :Optional :Input:Array
+ [-o[utput] Out (stdout ).as(outFile::ASCII ) ] :Optional :Output: PCA
+ [-O[utput] Out2 (stdout ).as(outFile::ASCII ) ] :Optional :Output: Transform
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: bin2mrc
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: clusterLog2ToLog
Options:
- [-i[nput] In (stdin )] :Optional :Input: Log2
- [-o[utput] Out (stdout )] :Optional :Output: Log
- [-lastNum lastNum (1 )] :Optional :lastClusterNumber
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (stdin ).as(inFile ) ] :Optional :Input: Log2
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: Log
+ [-lastNum lastNum (1 ).as(Integer ) ] :Optional :lastClusterNumber
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: clusterLogASCII2Binary
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: ASCII LogFile
+ [-o[utput] Out (log ).as(String ) ] :Essential :Output: Binary LogFile BaseName
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: clusterShow
Options:
- [-i[nput] In (NULL )] :Optional :InputData: ASCII Log: Need -i, -i2, or -ib
- [-i[nput]2 In2 (NULL )] :Optional :InputData: ASCII Log2
- [-i[nput]b[inary] InB (NULL )] :Optional :InputData: BinaryLog: basename
- [-o[utput] Out (stdout )] :Optional :Output: All
- [-O[utput] Out2 (stdout )] :Optional :Output: ClusterOnly
- [-PS[output] OutPS (stdout )] :Optional :Output: ClusterForPS: Need -I
- [-O[utput]L[ist] OutOL (stdout )] :Optional :Output: ClusterList
- [-O[utput]T[reeInfo] TreeInfo (NULL )] :Optional :Output: TreeInfo
- [-A[verage]L[ist] OutAL (stdout )OutALRange (0 )OutALSuffix (avg )] :Optional :Output: ClusterList range
- [-Last[ClusterNumber]LastNum (1 )] :Optional :Last: Num
- [-S[cale] ShoulderScale (1 )ArmScale (1 )] :Optional :Scale: Shoulder Arm
- [-P[osition] PosX (0 )PosY (0 )] :Optional :Position: X Y
- [-Offset Offset (1 )] :Optional :Offset: Arm
- [-I[nfileList] InList (NULL )] :Optional :FileList
- [-Log ] :Optional :Arm: Log Scale
- [-Scaling ] :Optional :with Scaling
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputData: ASCII Log: Need -i, -i2, or -ib
+ [-i[nput]2 In2 (NULL ).as(inFile ) ] :Optional :InputData: ASCII Log2
+ [-i[nput]b[inary] InB (NULL ).as(String ) ] :Optional :InputData: BinaryLog: basename
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: All
+ [-O[utput] Out2 (stdout ).as(outFile ) ] :Optional :Output: ClusterOnly
+ [-PS[output] OutPS (stdout ).as(outFile ) ] :Optional :Output: ClusterForPS: Need -I
+ [-O[utput]L[ist] OutOL (stdout ).as(outFile ) ] :Optional :Output: ClusterList
+ [-O[utput]T[reeInfo] TreeInfo (NULL ).as(outFile ) ] :Optional :Output: TreeInfo
+ [-A[verage]L[ist] OutAL (stdout ).as(outFile )
+ OutALRange (0 ).as(Integer )
+ OutALSuffix (avg ).as(String ) ] :Optional :Output: ClusterList range
+ [-Last[ClusterNumber]LastNum (1 ).as(Integer ) ] :Optional :Last: Num
+ [-S[cale] ShoulderScale (1 ).as(Real )
+ ArmScale (1 ).as(Real ) ] :Optional :Scale: Shoulder Arm
+ [-P[osition] PosX (0 ).as(Real )
+ PosY (0 ).as(Real ) ] :Optional :Position: X Y
+ [-Offset Offset (1 ).as(Real ) ] :Optional :Offset: Arm
+ [-I[nfileList] InList (NULL ).as(inFileListNoOpen ) ] :Optional :FileList
+ [-Log ] :Optional :Arm: Log Scale
+ [-Scaling ] :Optional :with Scaling
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: coordRotation
Options:
- [-p x (0 )y (0 )z (0 )] :Essential :Point:
- [-mat[rix] Mat (stdin )] :Essential :Input: matrix
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-p x (0 ).as(Real )
+ y (0 ).as(Real )
+ z (0 ).as(Real ) ] :Essential :Point:
+ [-mat[rix] Mat (stdin ).as(inFile ) ] :Essential :Input: matrix
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: ctfDeterminationFromMultiImage
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrcImageList
- [-o[utput] Out (stdout )] :Optional :Output: Result obtained by fitting procedure
- [-O[utput] Out2 (.estimate )] :Optional :Output: Estimated scattering: add this value to input filename
- [-Molec[ular]Env[elope]MolecEnv (50 )] :Optional :Input [A]: Spread : Assign molecular envelope as Gaussian
- [-Molec[ular]Env[elope]2MolecEnvFile (NULL )] :Optional :Input filename: Scattering Factor suggested by Table
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFileList ) ] :Optional :Input: mrcImageList
+ [-i[nput] In2 (NULL ).as(inFileList ) ] :Optional :Input: AngularDistributionList
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: Result obtained by fitting procedure
+ [-O[utput] Out2 (.estimate ).as(String ) ] :Optional :Output: Estimated scattering: add this value to input filename
+ [-Molec[ular]Env[elope]MolecEnv (50 ).as(Real ) ] :Optional :Input [A]: Spread : Assign molecular envelope as Gaussian
+ [-Molec[ular]Env[elope]2MolecEnvFile (NULL ).as(String ) ] :Optional :Input filename: Scattering Factor suggested by Table
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- InFile format: -i or -i2
filename defocus[A] AmpOverPhase kV Cs Cc Ai I SN MTFMode MTF MTF2 MolecEnv Magnification
<PRE>
Usage: ctfDeterminationFromThonRing
Options:
- [-i[nput] In (stdin )] :Optional :InputDataFile
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-oP[utput] Out2 (NULL )] :Optional :OutputParameter
- [-kV kV (200 )] :Optional :kV
- [-Cs Cs (1.7 )] :Optional :Cs[mm]
- [-Def minDef (0.0 )maxDef (200000.0 )delDef (1000.0 )] :Optional :Def[A]
- [-Amp minAmp (0.0 )maxAmp (0.4 )delAmp (0.005 )] :Optional :AmpToPhase
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-R[/A] R (NULL )... ] :Variable :ThonRing[/A]
+ [-i[nput] In (stdin ).as(inFile ) ] :Optional :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-oP[utput] Out2 (NULL ).as(outFile ) ] :Optional :OutputParameter
+ [-kV kV (200 ).as(Real ) ] :Optional :kV
+ [-Cs Cs (1.7 ).as(Real ) ] :Optional :Cs[mm]
+ [-Def minDef (0.0 ).as(Real )
+ maxDef (200000.0 ).as(Real )
+ delDef (1000.0 ).as(Real ) ] :Optional :Def[A]
+ [-Amp minAmp (0.0 ).as(Real )
+ maxAmp (0.4 ).as(Real )
+ delAmp (0.005 ).as(Real ) ] :Optional :AmpToPhase
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-R[/A] R (NULL ).as(Real ) ... ] :Variable :ThonRing[/A]
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: ctfDetermine
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile: mrcImage
- [-o[utput] Out (NULL )] :Essential :OutputDataFile: Parameters
- [-D[efocus] Defocus (0.0 )] :Optional :InitialDefocus[A]
- [-Cs Cs (1.7 )] :Optional :InitialCs[mm]
- [-Cc Cc (1.2 )] :Optional :InitialCs[mm]
- [-dE dE (0.2 )] :Optional :InitialCs[mm]
- [-Ac[cerratedVoltage]Ac (200 )] :Optional :Ac[kV]
- [-CutLow CutLow (0.05 )] :Optional :CutOffLowFrequncy[/A]
- [-CutHigh CutHigh (0.5 )] :Optional :CutOffHighFrequncy[/A]
- [-I0 I0 (1.0 )] :Optional :I0
- [-ratio ratioOfAmpToPhase (0.1 )] :Optional :ratioOfAmpToPhase
- [-Ai Ai (0.03 )] :Optional :IlluminationAngle[mrad]
- [-BofMTF BofMTF (15.0 )] :Optional :B of MTF [A]
- [-BofV[ibration] BofVibration (3.0 )] :Optional :B of Vibration [A]
- [-Mag[nification] Magnification (1.0 )] :Optional :Magnification
- [-[White]Noise WhiteNoise (0.0 )] :Optional :Signal/Noise Ratio
- [-[White]Noise2 WhiteNoise2 (0.0 )] :Optional :Signal/Noise Ratio
- [-MolcEnv MolcEnv (0.0 )] :Optional :Gaussian: Molcular Envelop [A]
- [-MolcEnv2 MolcEnvTable (NULL )] :Optional :Table: Molcular Envelop
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-min min (-10 )] :Optional :min of coefficient area
- [-max max (10 )] :Optional :max of coefficient area
- [-s[tep] step (0.01 )] :Optional :step of coefficient
- [-d[egree] degree (6 )] :Optional :agree of function
- [-S[ection] section (4 )] :Optional :section number of fft
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile: mrcImage
+ [-o[utput] Out (NULL ).as(appendFile ) ] :Essential :OutputDataFile: Parameters
+ [-D[efocus] Defocus (0.0 ).as(Real ) ] :Optional :InitialDefocus[A]
+ [-Cs Cs (1.7 ).as(Real ) ] :Optional :InitialCs[mm]
+ [-Cc Cc (1.2 ).as(Real ) ] :Optional :InitialCs[mm]
+ [-dE dE (0.2 ).as(Real ) ] :Optional :InitialCs[mm]
+ [-Ac[cerratedVoltage]Ac (200 ).as(Real ) ] :Optional :Ac[kV]
+ [-CutLow CutLow (0.05 ).as(Real ) ] :Optional :CutOffLowFrequncy[/A]
+ [-CutHigh CutHigh (0.5 ).as(Real ) ] :Optional :CutOffHighFrequncy[/A]
+ [-I0 I0 (1.0 ).as(Real ) ] :Optional :I0
+ [-ratio ratioOfAmpToPhase (0.1 ).as(Real ) ] :Optional :ratioOfAmpToPhase
+ [-Ai Ai (0.03 ).as(Real ) ] :Optional :IlluminationAngle[mrad]
+ [-BofMTF BofMTF (15.0 ).as(Real ) ] :Optional :B of MTF [A]
+ [-BofV[ibration] BofVibration (3.0 ).as(Real ) ] :Optional :B of Vibration [A]
+ [-Mag[nification] Magnification (1.0 ).as(Real ) ] :Optional :Magnification
+ [-[White]Noise WhiteNoise (0.0 ).as(Real ) ] :Optional :Signal/Noise Ratio
+ [-[White]Noise2 WhiteNoise2 (0.0 ).as(Real ) ] :Optional :Signal/Noise Ratio
+ [-MolcEnv MolcEnv (0.0 ).as(Real ) ] :Optional :Gaussian: Molcular Envelop [A]
+ [-MolcEnv2 MolcEnvTable (NULL ).as(inFile ) ] :Optional :Table: Molcular Envelop
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-min min (-10 ).as(Real ) ] :Optional :min of coefficient area
+ [-max max (10 ).as(Real ) ] :Optional :max of coefficient area
+ [-s[tep] step (0.01 ).as(Real ) ] :Optional :step of coefficient
+ [-d[egree] degree (6 ).as(Integer ) ] :Optional :agree of function
+ [-S[ection] section (4 ).as(Integer ) ] :Optional :section number of fft
>>> Mode <<<
0 : MinMax Methods (Henderson-like CTF determination)
16: Fitting Methods
<PRE>
Usage: ctfDisplay
Options:
- [-i[nput] inMRC (NULL )] :Optional :Input:MRC(FFT)
- [-o[utput] outCTF (stdout )] :Optional :Input/Output: ctfinfo
- [-Rmax Rmax (0.2 )] :Optional :Rmax [A-1]
- [-Imax Imax (0.2 )] :Optional :Intensity: min-max
- [-Imin Imin (0.02 )] :Optional :Intensity: min-max
- [-AutoRange ] :Optional :Intensity: min-max
- [-Log ] :Optional :Log of Intensity
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] inMRC (NULL ).as(inFile ) ] :Optional :Input:MRC(FFT)
+ [-o[utput] outCTF (stdout ).as(appendFile ) ] :Optional :Input/Output: ctfinfo
+ [-Rmax Rmax (0.2 ).as(Real ) ] :Optional :Rmax [A-1]
+ [-Imax Imax (0.2 ).as(Real ) ] :Optional :Intensity: min-max
+ [-Imin Imin (0.02 ).as(Real ) ] :Optional :Intensity: min-max
+ [-AutoRange ] :Optional :Intensity: min-max
+ [-Log ] :Optional :Log of Intensity
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: ctfEnvelopFunction
Options:
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-Rmax Rmax (0.1 )] :Optional :Rmax[/A]
- [-dR dR (0.0001 )] :Optional :dR[/A]
- [-kV kV (200 )] :Optional :AccVol[kV]
- [-Cs Cs (1.7 )] :Optional :Cs[mm]
- [-df Defocus (100000 )] :Essential :Defocus[A]:under(+)
- [-A AoverP (0.0 )] :Optional :AmplitudeContrast/PhaseContrast
- [-Ain Ain (0.02 )] :Optional :IlluminationAperture[mrad]
- [-ctfMode ctfMode (32 )] :Optional :CTFMode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-Rmax Rmax (0.1 ).as(Real ) ] :Optional :Rmax[/A]
+ [-dR dR (0.0001 ).as(Real ) ] :Optional :dR[/A]
+ [-kV kV (200 ).as(Real ) ] :Optional :AccVol[kV]
+ [-Cs Cs (1.7 ).as(Real ) ] :Optional :Cs[mm]
+ [-df Defocus (100000 ).as(Real ) ] :Essential :Defocus[A]:under(+)
+ [-A AoverP (0.0 ).as(Real ) ] :Optional :AmplitudeContrast/PhaseContrast
+ [-Ain Ain (0.02 ).as(Real ) ] :Optional :IlluminationAperture[mrad]
+ [-ctfMode ctfMode (32 ).as(Integer ) ] :Optional :CTFMode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
>>>> ctfMode <<<<
ctfInfoModeWithIlluminationAngle 32
ctfInfoModeWithEnergySpread 64
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>ctfEnvelopFunctionEstimate</TITLE>
+</HEAD>
+<BODY>
+<H1>ctfEnvelopFunctionEstimate</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ctfEnvelopFunctionEstimate
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:
+ [-o[utput] Out (stdout ).as(outFile::ASCII ) ] :Optional :Output:
+ [-degree degree (6 ).as(Integer ) ] :Optional :[dim]
+ [-Range CutLow (0.01 ).as(Real )
+ CutHigh (0.2 ).as(Real ) ] :Optional :[/A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: ctfFunction
Options:
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-Rmax Rmax (0.1 )] :Optional :Rmax[/A]
- [-dR dR (0.0001 )] :Optional :dR[/A]
- [-kV kV (200 )] :Optional :AccVol[kV]
- [-Cs Cs (2.1 )] :Optional :Cs[mm]
- [-df Defocus (27000 )] :Essential :Defocus[A]:under(+)
- [-A AoverP (0.0 )] :Optional :AmplitudeContrast/PhaseContrast
- [-Ain Ain (0.02 )] :Optional :IlluminationAperture[mrad]
- [-ctfMode ctfMode (32 )] :Optional :CTFMode
- [-pvm pvm (0 )] :Optional :PVM: MultiProcessor
- [-pvmList pvmList (stdin )] :Optional :PVM Host List: MultiProcessor
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-Rmax Rmax (0.1 ).as(Real ) ] :Optional :Rmax[/A]
+ [-dR dR (0.0001 ).as(Real ) ] :Optional :dR[/A]
+ [-kV kV (200 ).as(Real ) ] :Optional :AccVol[kV]
+ [-Cs Cs (2.1 ).as(Real ) ] :Optional :Cs[mm]
+ [-df Defocus (27000 ).as(Real ) ] :Essential :Defocus[A]:under(+)
+ [-A AoverP (0.0 ).as(Real ) ] :Optional :AmplitudeContrast/PhaseContrast
+ [-Ain Ain (0.02 ).as(Real ) ] :Optional :IlluminationAperture[mrad]
+ [-ctfMode ctfMode (32 ).as(Integer ) ] :Optional :CTFMode
+ [-pvm pvm (0 ).as(Integer ) ] :Optional :PVM: MultiProcessor
+ [-pvmList pvmList (stdin ).as(inFile ) ] :Optional :PVM Host List: MultiProcessor
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
>>>> ctfMode <<<<
0: Phase CTF
1: PhaseCTF + ratio*AmpCTF
<PRE>
Usage: ctfInfoSet
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: ctfMultiFunction
Options:
- [-I[nput array of file]In (NULL )] :Optional :InputDataFiles
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-Rmax Rmax (0.1 )] :Optional :Rmax[/A]
- [-dR dR (0.0001 )] :Optional :dR[/A]
- [-Ain Ain (0.02 )] :Optional :IlluminationAperture[mrad]
- [-ctfMode ctfMode (33 )] :Optional :CTFMode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-I[nput array of file]In (NULL ).as(inFileListNoOpen ) ] :Optional :InputDataFiles
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-Rmax Rmax (0.1 ).as(Real ) ] :Optional :Rmax[/A]
+ [-dR dR (0.0001 ).as(Real ) ] :Optional :dR[/A]
+ [-Ain Ain (0.02 ).as(Real ) ] :Optional :IlluminationAperture[mrad]
+ [-ctfMode ctfMode (33 ).as(Integer ) ] :Optional :CTFMode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
>>>> ctfMode <<<<
0: Phase CTF
<PRE>
Usage: ctfWeightMapCreation
Options:
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-kV kV (200 )] :Optional :AccVol[kV]
- [-Cs Cs (1.7 )] :Optional :Cs[mm]
- [-df Defocus (2.7 )] :Essential :Defocus[A]:under(+)
- [-white WhiteNoise (1.0 )] :Optional :WhiteNoise(N/S)
- [-noise Noise (NULL )] :Optional :Noise Power Spectrum
- [-splusn SplusN (NULL )] :Optional :Signal+Noise Power Spectrum
- [-dRinv dRinv (1024*5/3 )] :Essential :dRinv[A]
- [-dRmaxInv dRmaxInv (10.0 )] :Essential :dRmaxInv[A]
- [-SinWin SinWinRminInv (20.0 )SinWinRmaxInv (10.0 )] :Optional :RminInv[A] RmaxInv[A]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-kV kV (200 ).as(Real ) ] :Optional :AccVol[kV]
+ [-Cs Cs (1.7 ).as(Real ) ] :Optional :Cs[mm]
+ [-df Defocus (2.7 ).as(Real ) ] :Essential :Defocus[A]:under(+)
+ [-white WhiteNoise (1.0 ).as(Real ) ] :Optional :WhiteNoise(N/S)
+ [-noise Noise (NULL ).as(inFile ) ] :Optional :Noise Power Spectrum
+ [-splusn SplusN (NULL ).as(inFile ) ] :Optional :Signal+Noise Power Spectrum
+ [-dRinv dRinv (1024*5/3 ).as(Real ) ] :Essential :dRinv[A]
+ [-dRmaxInv dRmaxInv (10.0 ).as(Real ) ] :Essential :dRmaxInv[A]
+ [-SinWin SinWinRminInv (20.0 ).as(Real )
+ SinWinRmaxInv (10.0 ).as(Real ) ] :Optional :RminInv[A] RmaxInv[A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
Mode:
0: No correction : F = G
1: Phase contrast : F = G*(H/abs(H))(Only 1 or -1)
<PRE>
Usage: defocusDeterminationFromThonRing
Options:
- [-i[nput] In (stdin )] :Optional :InputDataFile
- [-i[nput] N[ame] InN (stdin )] :Optional :InputNameInInformationFile
- [-i[nput] R[eference]InR (stdin )] :Optional :InputReferenceForLength
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-o[utput] I[nformation]OutI (stdout )] :Optional :OutputInformationFile
- [-o[utput] I[nformation]OutI2 (stdout )] :Optional :OutputInformationFile
- [-o[utput] I[nformation]OutI3 (stdout )] :Optional :OutputInformationFile
- [-kV kV (200 )] :Optional :kV
- [-Cs Cs (2.1 )] :Optional :Cs[mm]
- [-A[mplitude contrast]AoverP (0.05 )] :Optional :The ratio of amplitude contrast to phase contrast
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-ctfMode ctfMode (0 )] :Optional :CTFMode
- [-truePitch truePitch (430 )] :Optional :True Pitch
- [-PixelSize PixelSize (5 )] :Optional :Pixel Size [A]
- [-deltadY deltadY (0.5 )] :Optional :A range of deltadY to determine dY.
- [-R[/A] R (NULL )... ] :Variable :ThonRing[/A]
+ [-i[nput] In (stdin ).as(inFile ) ] :Optional :InputDataFile
+ [-i[nput] N[ame] InN (stdin ).as(String ) ] :Optional :InputNameInInformationFile
+ [-i[nput] R[eference]InR (stdin ).as(String ) ] :Optional :InputReferenceForLength
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-o[utput] I[nformation]OutI (stdout ).as(outFile ) ] :Optional :OutputInformationFile
+ [-o[utput] I[nformation]OutI2 (stdout ).as(outFile ) ] :Optional :OutputInformationFile
+ [-o[utput] I[nformation]OutI3 (stdout ).as(outFile ) ] :Optional :OutputInformationFile
+ [-kV kV (200 ).as(Real ) ] :Optional :kV
+ [-Cs Cs (2.1 ).as(Real ) ] :Optional :Cs[mm]
+ [-A[mplitude contrast]AoverP (0.05 ).as(Real ) ] :Optional :The ratio of amplitude contrast to phase contrast
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-ctfMode ctfMode (0 ).as(Integer ) ] :Optional :CTFMode
+ [-truePitch truePitch (430 ).as(Real ) ] :Optional :True Pitch
+ [-PixelSize PixelSize (5 ).as(Real ) ] :Optional :Pixel Size [A]
+ [-deltadY deltadY (0.5 ).as(Real ) ] :Optional :A range of deltadY to determine dY.
+ [-R[/A] R (NULL ).as(Real ) ... ] :Variable :ThonRing[/A]
----- Additional Usage -----
>>>> o[uput] I[nformation] <<<<
This file is used for [mrcImageMultiCTFCompensation and mrcImageCTFCompensation]
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>dm2mrc</TITLE>
+</HEAD>
+<BODY>
+<H1>dm2mrc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: dm2mrc
+Options:
+ [-i[nput] In (NULL ).as(inFile::dmFile ) ] :Essential :Input:dmFile(dm3|dm4)
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output:mrcImage
+ [-t[humnail] Thumnail (NULL ).as(outFile::mrcImage ) ] :Optional :Thumnail:mrcImage
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
+ -m 0 ; tagTerm: tagName/tagValue/.. etc
+ -m 1 ; tagName: tagValue etc
</PRE>
</BODY>
</HTML>
<PRE>
Usage: dos2unix
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: electronWaveLength
Options:
- [-kV kV (200 )] :Optional :InputDataFile
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-kV kV (200 ).as(Real ) ] :Optional :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: emData2mrc
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-m[agCorrection] magCorrection (1.0 )] :Optional :MagCorrection:
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-m[agCorrection] magCorrection (1.0 ).as(Real ) ] :Optional :MagCorrection:
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
-/bin/bash: energyTransferModelCheck: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>energyTransferModelCheck</TITLE>
+</HEAD>
+<BODY>
+<H1>energyTransferModelCheck</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: energyTransferModelCheck
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-p[db] PDB (NULL ).as(inFile ) ] :Optional :Excluded Area by PDB: Input[PDB]
+ [-P[dbs] PDBs (NULL ).as(inFileList ) ] :Optional :Excluded Area by PDB: Input[PDBFileList]
+ [-P[DBs]W[ithInfo] ] :Optional :PDBFileList With Info: filename sigma[A]
+ [-sigma sigma (1.0 ).as(Real ) ] :Optional :SigmaOfAtom for All: sigma [pixel]x delta[A/pixel]
+ [-sigmaA sigmaA (1.0 ).as(Real ) ] :Optional :SigmaOfAtom for All: sigma [A]
+ [-mrc MRC (NULL ).as(inFile ) ] :Optional :Excluded Area by mrc: Input[MRC]
+ [-MRC MRCs (NULL ).as(inFileList ) ] :Optional :Excluded Area by MRC: Input[MRCFileList]
+ [-MRCW[ithInfo] ] :Optional :MRCFileList with Info: filename contour near[A]
+ [-C[ontour] EContour (10. ).as(Real ) ] :Optional :ContourLevel for Exclusion: Density<ContourLevel -> 0
+ [-Near ENear (1. ).as(Real ) ] :Optional :Near [pixel]: Exclusion Area: near[pixel] x delta [A/pixel]
+ [-NearA ENearA (1. ).as(Real ) ] :Optional :Near [A]: Exclusion Area: near [A]
+ [-r[estrict] Rest (NULL ).as(inFile ) ] :Optional :Restricted Area: Input[mrc]
+ [-R[estrict] Rests (NULL ).as(inFileList ) ] :Optional :Restricted Area: InputDataFileList[mrcs]
+ [-contour Contour (10. ).as(Real ) ] :Optional :ContourLevel for Restriction
+ [-near Near (1. ).as(Real ) ] :Optional :Near [pixel]: Restriction Area: near[pixel] x delta [A/pixel]
+ [-nearA NearA (1. ).as(Real ) ] :Optional :Near [A]: Restriction Area: near[A]
+ [-R[estrictWithInfo] ] :Optional :WithInfo: filename contour near[A]
+ [-r[estrict]P RestP (NULL ).as(inFile ) ] :Optional :Restricted Area: InputDataFile[pdb]
+ [-R[estrict]P RestsP (NULL ).as(inFileList ) ] :Optional :Restricted Area: InputDataFileList[pdbs]: format: filename near[pixel]
+ [-sigmaP SigmaP (1. ).as(Real ) ] :Optional :Sigma[pixel]: Restriction Area: sigma x delta [A]
+ [-sigmaPA SigmaPA (1. ).as(Real ) ] :Optional :Sigma[A]: Restriction Area: sigma [A]
+ [-nearP NearP (1. ).as(Real ) ] :Optional :Near [pixel]: Restriction Area: near x delta [A]
+ [-nearPA NearPA (1. ).as(Real ) ] :Optional :Near [A]: Restriction Area: near [A]
+ [-R[estrict]PW ] :Optional :WithInfo: filename near[A] sigma[A]
+ [-delta deltax (5 ).as(Real )
+ deltay (5 ).as(Real )
+ deltaz (5 ).as(Real ) ] :Optional :delta [A]
+ [-sdelta sdeltax (5 ).as(Real )
+ sdeltay (5 ).as(Real )
+ sdeltaz (5 ).as(Real ) ] :Optional :starting delta [A]
+ [-start startx (5 ).as(Real )
+ starty (5 ).as(Real )
+ startz (5 ).as(Real ) ] :Optional :start [A]
+ [-end endx (5 ).as(Real )
+ endy (5 ).as(Real )
+ endz (5 ).as(Real ) ] :Optional :end [A]
+ [-maxIter maxIter (1 ).as(Integer ) ] :Optional :Max Iteration
+ [-startIter startIter (0 ).as(Integer ) ] :Optional :Start Iteration
+ [-neglect neglect (1e-4 ).as(Real ) ] :Optional :neglect: probability for each term: not final probability
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+----- Point Information : Each ID has no space character. -----
+ID fix x y z rootB radius(noUse)
+......
+ID unfix x y z rootB radius
+......
+ID connect ID length rootB
+......
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: energyTransferModelResultCheck
Options:
- [-i[nput] In (NULL )] :Essential :Input:
- [-I[nput] InResHead (test.out )] :Essential :Input: Result Filename Header
- [-I[nput]2 InResTail (0 )] :Optional :Input: Iteration Number
- [-neg[lect] Neg (1e-6 )] :Optional :Input: Neglect
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (1 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input:
+ [-I[nput] InResHead (test.out ).as(String ) ] :Essential :Input: Result Filename Header
+ [-I[nput]2 InResTail (0 ).as(Integer ) ] :Optional :Input: Iteration Number
+ [-neg[lect] Neg (1e-6 ).as(Real ) ] :Optional :Input: Neglect
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (1 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
--- /dev/null
+/bin/bash: eosBayesInit: No such file or directory
<PRE>
Usage: gmolvie
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
-<HTML>
-<HEAD>
-<TITLE>imagesView</TITLE>
-</HEAD>
-<BODY>
-<H1>imagesView</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: imagesView
-Options:
- [-i[nput] In (stdin )] :Optional :Input: FileList
- [-o[utput] Out (stdout )] :Optional :Output: FileViewCondition
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
-Additional Usage
-This command for viewing images with a suffix
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: imagesView: そのようなファイルやディレクトリはありません
<PRE>
Usage: imodst2mrc
Options:
- [-i[nput] In (NULL )] :Essential :Input: Imod Store
- [-o[utput] Out (NULL )] :Optional :Output: MRC
- [-O[utput] ] :Optional :Output: MRC LIST
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: Imod Store
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :Output: MRC
+ [-O[utput] ] :Optional :Output: MRC LIST
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: ip2mrc
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile[.img]
- [-i2[nput] InTem (NULL )] :Optional :InputDataFile[.tem]
- [-i3[nput] InInf (NULL )] :Optional :InputDataFile[.inf]
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-o2[utput] Out2 (NULL )] :Optional :OutputDataFile[1/4]
- [-Mag Mag (40000 )] :Optional :Magnification
- [-SE SE (200 )] :Optional :SE
- [-OutMode OutMode (1 )] :Optional :OutPutMode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile[.img]
+ [-i2[nput] InTem (NULL ).as(inFile ) ] :Optional :InputDataFile[.tem]
+ [-i3[nput] InInf (NULL ).as(inFile ) ] :Optional :InputDataFile[.inf]
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-o2[utput] Out2 (NULL ).as(outFile ) ] :Optional :OutputDataFile[1/4]
+ [-Mag Mag (40000 ).as(Real ) ] :Optional :Magnification
+ [-SE SE (200 ).as(Real ) ] :Optional :SE
+ [-OutMode OutMode (1 ).as(Integer ) ] :Optional :OutPutMode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
mode: 0: No Skip
mode: 1: Skip(128 byte)
<PRE>
Usage: largeIPInfo
Options:
- [-i[nput] In ] :Essential :InputDataFile
- [-o[utput] Out ] :Optional :OutputDataFile
- [-start startx starty ] :Optional :StartCoord
- [-step stepx stepy ] :Optional :StepCoord
- [-size width height ] :Optional :SizeCoord
- [-c[onfig] configFile ] :Optional :ConfigurationFile
- [-m[ode] mode ] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-start startx (0 ).as(Integer )
+ starty (0 ).as(Integer ) ] :Optional :StartCoord
+ [-step stepx (1 ).as(Integer )
+ stepy (1 ).as(Integer ) ] :Optional :StepCoord
+ [-size width (LARGE_IP_IMAGE_WIDTH).as(Integer )
+ height (LARGE_IP_IMAGE_HEIGHT).as(Integer ) ] :Optional :SizeCoord
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: ll2ltlg
Options:
- [-i[nput] In ] :Essential :InputDataFile
- [-o[utput] Out ] :Essential :OutputDataFile
- [-c[onfig] configFile ] :Optional :ConfigurationFile
- [-t[itle] Title ] :Optional :Title
- [-l[lMax] llMax ] :Optional :llMax
- [-D[elRInv] delRInv ] :Optional :delRInv[A]
- [-R[MaxInv] RMaxInv ] :Optional :RMaxInv[A]
- [-d[elr] delr ] :Optional :delr[A]
- [-r[Max] rMax ] :Optional :rMax[A]
- [-f[lagOutputInfo] flagOutputInfo ] :Optional :flagOutputInfo
- [-m[ode] mode ] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-t[itle] Title (NULL ).as(String ) ] :Optional :Title
+ [-l[lMax] llMax (1 ).as(Integer ) ] :Optional :llMax
+ [-D[elRInv] delRInv (1.0 ).as(Real ) ] :Optional :delRInv[A]
+ [-R[MaxInv] RMaxInv (1.0 ).as(Real ) ] :Optional :RMaxInv[A]
+ [-d[elr] delr (1.0 ).as(Real ) ] :Optional :delr[A]
+ [-r[Max] rMax (1.0 ).as(Real ) ] :Optional :rMax[A]
+ [-f[lagOutputInfo] flagOutputInfo (0 ).as(Integer ) ] :Optional :flagOutputInfo
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
>> controlFile Format : replaced by other options which are definitely shown.
Title [char*80]
<PRE>
Usage: llDataAverage
Options:
- [-M[odel] Model (NULL )] :Essential :Input: ModelFileName(llData)
- [-i[nput] In (NULL )] :Essential :Input: InputDataFile
- [-l[ayer] llInfo (NULL )] :Essential :Input: Layer Line Information
- [-A[verage] Ave (NULL )] :Essential :Output: Averaged File Name
- [-o[utput] OutParam (stdout )] :Optional :Output: FittedParameter
- [-o2[utput] OutParam2 (NULL )] :Optional :Output: FittedParameter(phi, z)
- [-O[utput] Out (NULL )] :Optional :Output: FittedData
- [-P2[plot] P2 (NULL )] :Optional :Output: P2PlotData
- [-t[ruePitch] truePitch (1.0 )] :Optional :True Pitch
- [-d[eltaR] dR (1.0 )] :Optional :deltaR
- [-r[adial] rmin (1.0 )rmax (1.0 )dr (1.0 )] :Optional :Radial[Ratio]
- [-p[hi] phimin (0.0 )phimax (180.0 )dphi (5.0 )] :Optional :Phi [degree]
- [-z[shift] zmin (0.0 )zmax (60.0 )dz (5.0 )] :Optional :z [A]
- [-withoutAntiPole ] :Optional :Not Allow Antipole
- [-C[utValue] CutValue (1.0 )] :Optional :CutValue
- [-pvm pvm (0 )] :Optional :PVM:
- [-pvmList pvmList (stdin )] :Optional :PVM: HostList
- [-pvmList Log (stdout )] :Optional :PVM: HostList
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-M[odel] Model (NULL ).as(inFile ) ] :Essential :Input: ModelFileName(llData)
+ [-i[nput] In (NULL ).as(inFileList ) ] :Essential :Input: InputDataFile
+ [-l[ayer] llInfo (NULL ).as(inFile ) ] :Essential :Input: Layer Line Information
+ [-A[verage] Ave (NULL ).as(outFile ) ] :Essential :Output: Averaged File Name
+ [-o[utput] OutParam (stdout ).as(appendFile ) ] :Optional :Output: FittedParameter
+ [-o2[utput] OutParam2 (NULL ).as(outFileList ) ] :Optional :Output: FittedParameter(phi, z)
+ [-O[utput] Out (NULL ).as(outFileList ) ] :Optional :Output: FittedData
+ [-P2[plot] P2 (NULL ).as(outFile ) ] :Optional :Output: P2PlotData
+ [-t[ruePitch] truePitch (1.0 ).as(Real ) ] :Optional :True Pitch
+ [-d[eltaR] dR (1.0 ).as(Real ) ] :Optional :deltaR
+ [-r[adial] rmin (1.0 ).as(Real )
+ rmax (1.0 ).as(Real )
+ dr (1.0 ).as(Real ) ] :Optional :Radial[Ratio]
+ [-p[hi] phimin (0.0 ).as(Real )
+ phimax (180.0 ).as(Real )
+ dphi (5.0 ).as(Real ) ] :Optional :Phi [degree]
+ [-z[shift] zmin (0.0 ).as(Real )
+ zmax (60.0 ).as(Real )
+ dz (5.0 ).as(Real ) ] :Optional :z [A]
+ [-withoutAntiPole ] :Optional :Not Allow Antipole
+ [-C[utValue] CutValue (1.0 ).as(Real ) ] :Optional :CutValue
+ [-pvm pvm (0 ).as(Integer ) ] :Optional :PVM:
+ [-pvmList pvmList (stdin ).as(inFile ) ] :Optional :PVM: HostList
+ [-pvmList Log (stdout ).as(appendFile ) ] :Optional :PVM: HostList
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: llDataAxisSearch
Options:
- [-i1[nput] In1 (NULL )] :Optional :In: NearSide
- [-i2[nput] In2 (NULL )] :Optional :In: FarSide
- [-o1[utput] Out1 (NULL )] :Optional :Out: NearSide
- [-o2[utput] Out2 (NULL )] :Optional :Out: FarSide
- [-a[verage] Avg (NULL )] :Optional :Out: Average
- [-o[utput] Out (NULL )] :Optional :Out: FitParam
- [-op2[utput] OutP2 (NULL )] :Optional :OutParam2: FitParam Distribution [mrcImage]
- [-t[ruePitch] truePitch (0.0 )] :Optional :TruePitch[A]
- [-l[ayer] L (NULL )] :Optional :LayerInfo
- [-O[mega] Omin (0.0 )Omax (0.0 )Odelta (1.0 )] :Optional :Omega[degree]
- [-x[shift] xmin (-10.0 )xmax (10.0 )xdelta (0.1 )] :Optional :shiftx[A]
- [-R R (10.0 )] :Optional :Resolution[A]
- [-m[ode] mode (0 )] :Optional :Mode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-i1[nput] In1 (NULL ).as(inFile ) ] :Optional :In: NearSide
+ [-i2[nput] In2 (NULL ).as(inFile ) ] :Optional :In: FarSide
+ [-o1[utput] Out1 (NULL ).as(outFile ) ] :Optional :Out: NearSide
+ [-o2[utput] Out2 (NULL ).as(outFile ) ] :Optional :Out: FarSide
+ [-a[verage] Avg (NULL ).as(outFile ) ] :Optional :Out: Average
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :Out: FitParam
+ [-op2[utput] OutP2 (NULL ).as(outFile ) ] :Optional :OutParam2: FitParam Distribution [mrcImage]
+ [-t[ruePitch] truePitch (0.0 ).as(Real ) ] :Optional :TruePitch[A]
+ [-l[ayer] L (NULL ).as(inFile ) ] :Optional :LayerInfo
+ [-O[mega] Omin (0.0 ).as(Real )
+ Omax (0.0 ).as(Real )
+ Odelta (1.0 ).as(Real ) ] :Optional :Omega[degree]
+ [-x[shift] xmin (-10.0 ).as(Real )
+ xmax (10.0 ).as(Real )
+ xdelta (0.1 ).as(Real ) ] :Optional :shiftx[A]
+ [-R R (10.0 ).as(Real ) ] :Optional :Resolution[A]
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
----- Layer Line Information File -----
L N Weight
..........
<PRE>
Usage: llDataCTFCompensate
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-I[nput] In1 (NULL )] :Optional :InputCTFInformation
- [-I2[nput] In2 (NULL )] :Optional :InputCTFInformation2
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-t[ruePitch] truePitch (430.0 )] :Essential :truePitch[A]
- [-m[ode] mode (0 )] :Optional :Mode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-I[nput] In1 (NULL ).as(inFile ) ] :Optional :InputCTFInformation
+ [-I2[nput] In2 (NULL ).as(inFile ) ] :Optional :InputCTFInformation2
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-t[ruePitch] truePitch (430.0 ).as(Real ) ] :Essential :truePitch[A]
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
----- CTFInformation file 1 -----
RR0 F0 PHI0 : If R.lt.RR0, F0=0; If RR0.le.R.lt.RR1, Linear Interpolation F0, F1
RR1 F1 PHI1 : If RR1.le.R <RR2,
<PRE>
Usage: llDataCompare
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFileList
- [-r[eference] Ref (NULL )] :Essential :InputReferenceDataFile
- [-o[utput] Out (NULL )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFileList ) ] :Essential :InputDataFileList
+ [-r[eference] Ref (NULL ).as(inFile ) ] :Essential :InputReferenceDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
Mode
0: Integral
<PRE>
Usage: llDataContributionCalcDifferentN
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: llDataDump
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-R[max] RMax (0.1 )] :Optional :[/A]
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-R[max] RMax (0.1 ).as(Real ) ] :Optional :[/A]
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: llDataEquatorAdd
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: llDataExtract
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-n n (0 )] :Optional :n
- [-l l (0 )] :Optional :l
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-n n (0 ).as(Real ) ] :Optional :n
+ [-l l (0 ).as(Real ) ] :Optional :l
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
input n and l
</PRE>
<PRE>
Usage: llDataFit
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: llDataInfo
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-l[ayer] layer (0 )] :Optional :LayerNumber
- [-L[ayer] NN (0 )LL (0 )] :Optional :LayerInfo
- [-m[ode] mode (0 )] :Optional :Mode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-l[ayer] layer (0 ).as(Integer ) ] :Optional :LayerNumber
+ [-L[ayer] NN (0 ).as(Integer )
+ LL (0 ).as(Integer ) ] :Optional :LayerInfo
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
----- mode -----
1 : Total Layer Line Infomation
2 : Information of Each Layer Line
<PRE>
Usage: llDataLowPassFiltering
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-t[ruePitch] truePitch (760 )] :Essential :[A]
- [-R[max] RMax (0.1 )] :Optional :[/A]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-t[ruePitch] truePitch (760 ).as(Real ) ] :Essential :[A]
+ [-R[max] RMax (0.1 ).as(Real ) ] :Optional :[/A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
-m 0: SameMemorySize data
-m 1: SavedMemorySize data
<PRE>
Usage: llDataMultiCTFCompensation
Options:
- [-i[nput] In (NULL )] :Essential :Input: FileList
- [-M[odel] Ref (NULL )] :Essential :Input: Model Data
- [-l[ayerLine] llInfo (NULL )] :Essential :Input: Layer Line Information
- [-A[verageFile] Ave (NULL )] :Essential :Output: AverageFile
- [-o[utput] OutParam (NULL )] :Optional :Output: FittedParameter
- [-O[utput] Out (NULL )] :Optional :Output: FileList: PhaseShift of Each Filament
- [-o2[utput] OutParam2 (NULL )] :Optional :Output: [phi, z] map
- [-P2[output] OutParamP2 (NULL )] :Optional :Output: For P-P'
- [-N[oise] Noise (0.0 )] :Optional :Noise Ratio
- [-t[ruePitch] truePitch (761.4 )] :Essential :truePitch[A]
- [-d[eltaR] deltaR (1.0 )] :Optional :deltaR[A]
- [-r[adial] rmin (1.0 )rmax (1.0 )dr (1.0 )] :Optional :Radial[Ratio]
- [-p[hi] phimin (0.0 )phimax (180.0 )dphi (1.0 )] :Optional :Phi [degree]
- [-z[shift] zmin (0.0 )zmax (180.0 )dz (1.0 )] :Optional :z [A]
- [-Rmax Rmax (0.1 )] :Optional :Rmax [/A]
- [-MaxIter[ation] MaxIter (1 )] :Optional :MaxIteration
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFileList ) ] :Essential :Input: FileList
+ [-M[odel] Ref (NULL ).as(inFile ) ] :Essential :Input: Model Data
+ [-l[ayerLine] llInfo (NULL ).as(inFile ) ] :Essential :Input: Layer Line Information
+ [-A[verageFile] Ave (NULL ).as(outFile ) ] :Essential :Output: AverageFile
+ [-o[utput] OutParam (NULL ).as(appendFile ) ] :Optional :Output: FittedParameter
+ [-O[utput] Out (NULL ).as(outFileList ) ] :Optional :Output: FileList: PhaseShift of Each Filament
+ [-o2[utput] OutParam2 (NULL ).as(outFileList ) ] :Optional :Output: [phi, z] map
+ [-P2[output] OutParamP2 (NULL ).as(outFile ) ] :Optional :Output: For P-P'
+ [-N[oise] Noise (0.0 ).as(Real ) ] :Optional :Noise Ratio
+ [-t[ruePitch] truePitch (761.4 ).as(Real ) ] :Essential :truePitch[A]
+ [-d[eltaR] deltaR (1.0 ).as(Real ) ] :Optional :deltaR[A]
+ [-r[adial] rmin (1.0 ).as(Real )
+ rmax (1.0 ).as(Real )
+ dr (1.0 ).as(Real ) ] :Optional :Radial[Ratio]
+ [-p[hi] phimin (0.0 ).as(Real )
+ phimax (180.0 ).as(Real )
+ dphi (1.0 ).as(Real ) ] :Optional :Phi [degree]
+ [-z[shift] zmin (0.0 ).as(Real )
+ zmax (180.0 ).as(Real )
+ dz (1.0 ).as(Real ) ] :Optional :z [A]
+ [-Rmax Rmax (0.1 ).as(Real ) ] :Optional :Rmax [/A]
+ [-MaxIter[ation] MaxIter (1 ).as(Integer ) ] :Optional :MaxIteration
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
---- InputFileFormat ----
filename weight(NumberOfAveragedFile) deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
----- Mode -----
<PRE>
Usage: llDataNEstimation
Options:
- [-r[peak] r (220 )] :Essential :Input: rpeak [A]
- [-R[peak] R (24 )] :Essential :Input: Rpeak [pixel]
- [-xstep xstep (7 )] :Essential :Input: xstep [A]
- [-W[idth] Width (500 )] :Essential :Input: Width [pixel]
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-r[peak] r (220 ).as(Real ) ] :Essential :Input: rpeak [A]
+ [-R[peak] R (24 ).as(Real ) ] :Essential :Input: Rpeak [pixel]
+ [-xstep xstep (7 ).as(Real ) ] :Essential :Input: xstep [A]
+ [-W[idth] Width (500 ).as(Real ) ] :Essential :Input: Width [pixel]
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: llDataNormalization
Options:
- [-i[nput] In (NULL )] :Essential :llData:InputDataFile
- [-r[eference] Ref (NULL )] :Essential :llData:Reference
- [-o[utput] Out (NULL )] :Optional :llData(Normalized In):OutputDataFile
- [-dif[ffence] Dif (NULL )] :Optional :llData(Difference):OutputDataFile
- [-O[utput] OutParam (stdout )] :Optional :FittedParameter
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :llData:InputDataFile
+ [-r[eference] Ref (NULL ).as(inFile ) ] :Essential :llData:Reference
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :llData(Normalized In):OutputDataFile
+ [-dif[ffence] Dif (NULL ).as(outFile ) ] :Optional :llData(Difference):OutputDataFile
+ [-O[utput] OutParam (stdout ).as(outFile ) ] :Optional :FittedParameter
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
-<HTML>
-<HEAD>
-<TITLE>llDataPrint</TITLE>
-</HEAD>
-<BODY>
-<H1>llDataPrint</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: llDataPrint
-Options:
- [-i[nput] In (NULL )] :Optional :InputDataFile
- [-i[nput]s Ins (NULL )] :Optional :InputDataFileList
- [-i2[nput] Nea (NULL )Far (NULL )] :Optional :InputDataFile(nea and far)
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-Rmax Rmax (0.1 )] :Optional :Input: Rmax [/A]
- [-I[nteractive] ] :Optional :Interactive
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: llDataPrint: そのようなファイルやディレクトリはありません
<PRE>
Usage: llDataRescaling
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-r[Scale] rScale (1.0 )] :Optional :[]
- [-dR delBR (0.0 /* No Change */)] :Optional :[/A]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-r[Scale] rScale (1.0 ).as(Real ) ] :Optional :[]
+ [-dR delBR (0.0 /* No Change */).as(Real ) ] :Optional :[/A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: llDataResolutionCheck
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFileList ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: llDataSelectionEstimation
Options:
- [-i1[nput] N1 (0 )L1 (161 )] :Essential :Input: N L
- [-i2[nput] N2 (14 )L2 (12 )] :Essential :Input: N L
- [-tmax tmax (100 )] :Optional :Input: tmax
- [-umax umax (200 )] :Optional :Input: umax
- [-r[accept] r (0.1 )] :Optional :Input: acceptable residue
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i1[nput] N1 (0 ).as(Real )
+ L1 (161 ).as(Real ) ] :Essential :Input: N L
+ [-i2[nput] N2 (14 ).as(Real )
+ L2 (12 ).as(Real ) ] :Essential :Input: N L
+ [-tmax tmax (100 ).as(Real ) ] :Optional :Input: tmax
+ [-umax umax (200 ).as(Real ) ] :Optional :Input: umax
+ [-r[accept] r (0.1 ).as(Real ) ] :Optional :Input: acceptable residue
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: llDataWeightSet
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-l[ayerInfo] llInfo (NULL )] :Optional :LayerInfomationFile
- [-w[eight] weight (1.0 )] :Optional :DefaultWeight
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-l[ayerInfo] llInfo (NULL ).as(inFile ) ] :Optional :LayerInfomationFile
+ [-w[eight] weight (1.0 ).as(Real ) ] :Optional :DefaultWeight
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: llDatarMaxLimit
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-r[Max] rMax (100.0 )] :Optional :rMax[A]
- [-rMin[Max] rMaxMin (100.0 )] :Optional :rMaxMin[A]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-r[Max] rMax (100.0 ).as(Real ) ] :Optional :rMax[A]
+ [-rMin[Max] rMaxMin (100.0 ).as(Real ) ] :Optional :rMaxMin[A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- rMax Limit Algorithm-----
<PRE>
Usage: llExtractCtfinfFileCreate
Options:
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-FirstZero FirstZero (0.02 )] :Optional :FirstZeroPoint[1/A]
- [-df Defocus (27000 )] :Optional :Defocus[A]:under(+)
- [-A AoverP (0.05 )] :Optional :AmplitudeContrast/PhaseContrast
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-FirstZero FirstZero (0.02 ).as(Real ) ] :Optional :FirstZeroPoint[1/A]
+ [-df Defocus (27000 ).as(Real ) ] :Optional :Defocus[A]:under(+)
+ [-A AoverP (0.05 ).as(Real ) ] :Optional :AmplitudeContrast/PhaseContrast
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- mode -----
0: make CTFInformation file 1
<PRE>
Usage: llExtractCtrlFileCreate
Options:
- [-i[nput] In (NULL )] :Optional :InputDataFile
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-t turn (-6 )] :Optional :Turn
- [-u unit (13 )] :Optional :Unit
- [-N nstrand (1 )] :Optional :N-strand
- [-Y1 Y1 (36 )] :Optional :Y1 [pixel]: The Position of LayerLine which l = |t| i.e., |n|=1&&m=0 for the first time
- [-Y0 Y0 (78 )] :Optional :Y0 [pixel]: The Position of LayerLine which n = 0 , l != 0 for the first time
- [-rmax rmax (250 )] :Optional :rmax[A]
- [-Rmax Rmax (0.1 )] :Optional :Rmax[/A]
- [-lx lx (5.0 )] :Optional :Pixel Size
- [-ly ly (5.0 )] :Optional :Pixel Size
- [-nx nx (1000.0 )] :Optional :Image Size[Pixel]
- [-ny ny (1000.0 )] :Optional :Image Size[Pixel]
- [-center center (500.0 )] :Optional :Center of nx (center of filament)[Pixel]
- [-layerline layerline (21.0 )] :Optional :Number of Layer Line
- [-Ax Ax (5000.0 )] :Optional :Length of nx (lx * nx)[A]
- [-dY dY (12.0 )] :Optional :Range of Layer Line[pixel]
- [-truePitch truePitch (430 )] :Optional :True Pitch
- [-PixelSize PixelSize (5 )] :Optional :Pixel Size [A]
- [-deltadY deltadY (0.5 )] :Optional :A range of deltadY to determine dY.[pixel]
- [-m[ode] mode (1 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-t turn (-6 ).as(Integer ) ] :Optional :Turn
+ [-u unit (13 ).as(Integer ) ] :Optional :Unit
+ [-N nstrand (1 ).as(Integer ) ] :Optional :N-strand
+ [-Y1 Y1 (36 ).as(Integer ) ] :Optional :Y1 [pixel]: The Position of LayerLine which l = |t| i.e., |n|=1&&m=0 for the first time
+ [-Y0 Y0 (78 ).as(Integer ) ] :Optional :Y0 [pixel]: The Position of LayerLine which n = 0 , l != 0 for the first time
+ [-rmax rmax (250 ).as(Real ) ] :Optional :rmax[A]
+ [-Rmax Rmax (0.1 ).as(Real ) ] :Optional :Rmax[/A]
+ [-lx lx (5.0 ).as(Real ) ] :Optional :Pixel Size
+ [-ly ly (5.0 ).as(Real ) ] :Optional :Pixel Size
+ [-nx nx (1000.0 ).as(Real ) ] :Optional :Image Size[Pixel]
+ [-ny ny (1000.0 ).as(Real ) ] :Optional :Image Size[Pixel]
+ [-center center (500.0 ).as(Real ) ] :Optional :Center of nx (center of filament)[Pixel]
+ [-layerline layerline (21.0 ).as(Real ) ] :Optional :Number of Layer Line
+ [-Ax Ax (5000.0 ).as(Real ) ] :Optional :Length of nx (lx * nx)[A]
+ [-dY dY (12.0 ).as(Real ) ] :Optional :Range of Layer Line[pixel]
+ [-truePitch truePitch (430 ).as(Real ) ] :Optional :True Pitch
+ [-PixelSize PixelSize (5 ).as(Real ) ] :Optional :Pixel Size [A]
+ [-deltadY deltadY (0.5 ).as(Real ) ] :Optional :A range of deltadY to determine dY.[pixel]
+ [-m[ode] mode (1 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- mode -----
0: for myosin t=1 u=9
<PRE>
Usage: llExtractWithLayerSeparation
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile(mrcImage:Fourier Space)
- [-I[nput] InLLNea (NULL )InLLFar (NULL )] :Optional :InputDataFile(llData:Already separated)
- [-r[ef] Ref (NULL )] :Optional :ReferenceData(llData:Gnl(R) Space)
- [-o[utput] Out (NULL )] :Essential :OutputDataFile(llData: Average File)
- [-o2[utput] Out2 (NULL )] :Optional :OutputDataFileList(llData: Each Filament which has the same orientation as average)
- [-o3[utput] Out3 (NULL )] :Optional :OutputDataFileList(llData: Difference of each filament)
- [-o4[utput] Out4 (NULL )] :Optional :OutputDataFileList(llData: Each Filament which has the same orientaion as original filament)
- [-o5[utput] Out5 (NULL )] :Optional :OutputDataFileList(mrcImage: P-Value)
- [-o6[utput] Out6 (NULL )] :Optional :OutputDataFileList(mrcImage: Q-Value)
- [-o7[utput] Out7 (NULL )] :Optional :OutputDataFile(Text: Two subsets for resolution estimation)
- [-o8[utput] Out8 (NULL )] :Optional :OutputDataFile(Text: For Back Projection)
- [-o9[utput] Out9 (NULL )] :Optional :OutputDataFileList(Text: x shift, z shift and dY information)
- [-comment InComment (NULL )] :Optional :Comment
- [-symmetry symmetry (1.0 )] :Optional :Symmetry for back projection text file
- [-l[ayerInfo] llInfo (NULL )] :Essential :LayerLineInformation
- [-l[ayerInfo]final llInfoFinal (NULL )] :Optional :LayerLineInformation(Final)
- [-li[ayerInfo] llInfoImp (NULL )] :Optional :LayerLineInformationImportant
- [-liw[ayerInfo] liWeight (1.0 )] :Optional :Weight of Important Layer
- [-liwStart[ayerInfo] liWeightStart (1.0 )] :Optional :Weight of Important Layer
- [-liwStep[ayerInfo] liWeightStep (1.0 )] :Optional :Weight of Important Layer
- [-la[ayerInfo] llInfoAxis (NULL )] :Optional :LayerLineInformationForAxisSearch
- [-law[ayerInfo] laWeight (1.0 )] :Optional :Weight of Important Layer for AS
- [-lawStart[ayerInfo] laWeightStart (1.0 )] :Optional :Weight of Important Layer for AS
- [-lawStep[ayerInfo] laWeightStep (1.0 )] :Optional :Weight of Important Layer for AS
- [-truePitch truePitch (430.0 )] :Essential :true pitch [A]
- [-rMax rMax (100.0 )] :Essential :rMax [A]
- [-rMaxMin rMaxMin (100.0 )] :Optional :rMaxMin [A]
- [-RMax RMax (0.1 )] :Optional :RMax [/A]
- [-RMaxFirst RMaxFirst (0.04 )] :Optional :RMaxFirst [/A]: Def: RMax
- [-RMaxStep RMaxStep (0.02 )] :Optional :RMaxStep [/A]
- [-RRMax RRMax (0.1 )] :Optional :Radial RMax [/A]
- [-RRMaxFirst RRMaxFirst (0.04 )] :Optional :Radial RMaxFirst [/A]: Def: RMax
- [-RRMaxStep RRMaxStep (0.02 )] :Optional :Radial RMaxStep [/A]
- [-delBR delBR (0.0002 )] :Optional :delBR [/A]
- [-rms rms (1e-6 )] :Optional :rms:
- [-narrowSearch narrowSearch (1.0 )] :Optional :narrowSearch[Degree]: P-Value and Q-Value
- [-nextTimes nextTimes (1e-4 )] :Optional :nextTimes: rms
- [-maxIter[ation] MaxIteration (10 )] :Optional :max iteration:
- [-maxIter2[ation] MaxIter2 (1 )] :Optional :max iteration on the same RMax and RRMax:
- [-maxIter3[ation] MaxIter3 (1 )] :Optional :max iteration on the same RMax, RRMax, and Weight:
- [-lambda lambda (1.0 )] :Optional :labda:
- [-ctf CTF (0 )] :Optional :CTF Compensation
- [-WhiteNoise WhiteNoise (0.0 )] :Optional :White Noise
- [-below below (90.0 )] :Optional :below
- [-noantipole ] :Optional :No Antipole
- [-magLimit ] :Optional :magLimit
- [-eachTime ] :Optional :each time
- [-continue Continue (NULL )] :Optional :continue
- [-forContinue ForContinue (NULL )] :Optional :For continue
- [-phi phimin (0.0 )phimax (360.0 )delphi (10.0 )] :Optional :phi:[degree]
- [-z zmin (0.0 )zmax (30.0 )delz (5.0 )] :Optional :z:[A]
- [-shift shiftmin (-10.0 )shiftmax (10.0 )delshift (1.0 )] :Optional :shift:[A]
- [-log Log (stdout )] :Optional :LogFile
- [-Normalization ] :Optional :Normalization
- [-pvm pvm (0 )] :Optional :pvmNumber
- [-pvmList pvmList (NULL )] :Optional :pvmList
- [-pvmServer ] :Optional :Work as a server !!
- [-pvmClient ] :Optional :Work as a client !!
- [-wd WorkingDir (./ )] :Optional :Working Directory !!
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFileListNoOpen ) ] :Essential :InputDataFile(mrcImage:Fourier Space)
+ [-I[nput] InLLNea (NULL ).as(inFileListNoOpen )
+ InLLFar (NULL ).as(inFileListNoOpen ) ] :Optional :InputDataFile(llData:Already separated)
+ [-r[ef] Ref (NULL ).as(inFile ) ] :Optional :ReferenceData(llData:Gnl(R) Space)
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile(llData: Average File)
+ [-o2[utput] Out2 (NULL ).as(outFileListNoOpen ) ] :Optional :OutputDataFileList(llData: Each Filament which has the same orientation as average)
+ [-o3[utput] Out3 (NULL ).as(outFileListNoOpen ) ] :Optional :OutputDataFileList(llData: Difference of each filament)
+ [-o4[utput] Out4 (NULL ).as(outFileListNoOpen ) ] :Optional :OutputDataFileList(llData: Each Filament which has the same orientaion as original filament)
+ [-o5[utput] Out5 (NULL ).as(outFileListNoOpen ) ] :Optional :OutputDataFileList(mrcImage: P-Value)
+ [-o6[utput] Out6 (NULL ).as(outFileListNoOpen ) ] :Optional :OutputDataFileList(mrcImage: Q-Value)
+ [-o7[utput] Out7 (NULL ).as(outFile ) ] :Optional :OutputDataFile(Text: Two subsets for resolution estimation)
+ [-o8[utput] Out8 (NULL ).as(outFile ) ] :Optional :OutputDataFile(Text: For Back Projection)
+ [-o9[utput] Out9 (NULL ).as(outFileListNoOpen ) ] :Optional :OutputDataFileList(Text: x shift, z shift and dY information)
+ [-comment InComment (NULL ).as(String ) ] :Optional :Comment
+ [-symmetry symmetry (1.0 ).as(Real ) ] :Optional :Symmetry for back projection text file
+ [-l[ayerInfo] llInfo (NULL ).as(inFileListNoOpen ) ] :Essential :LayerLineInformation
+ [-l[ayerInfo]final llInfoFinal (NULL ).as(inFile ) ] :Optional :LayerLineInformation(Final)
+ [-li[ayerInfo] llInfoImp (NULL ).as(inFileListNoOpen ) ] :Optional :LayerLineInformationImportant
+ [-liw[ayerInfo] liWeight (1.0 ).as(Real ) ] :Optional :Weight of Important Layer
+ [-liwStart[ayerInfo] liWeightStart (1.0 ).as(Real ) ] :Optional :Weight of Important Layer
+ [-liwStep[ayerInfo] liWeightStep (1.0 ).as(Real ) ] :Optional :Weight of Important Layer
+ [-la[ayerInfo] llInfoAxis (NULL ).as(inFileListNoOpen ) ] :Optional :LayerLineInformationForAxisSearch
+ [-law[ayerInfo] laWeight (1.0 ).as(Real ) ] :Optional :Weight of Important Layer for AS
+ [-lawStart[ayerInfo] laWeightStart (1.0 ).as(Real ) ] :Optional :Weight of Important Layer for AS
+ [-lawStep[ayerInfo] laWeightStep (1.0 ).as(Real ) ] :Optional :Weight of Important Layer for AS
+ [-truePitch truePitch (430.0 ).as(Real ) ] :Essential :true pitch [A]
+ [-rMax rMax (100.0 ).as(Real ) ] :Essential :rMax [A]
+ [-rMaxMin rMaxMin (100.0 ).as(Real ) ] :Optional :rMaxMin [A]
+ [-RMax RMax (0.1 ).as(Real ) ] :Optional :RMax [/A]
+ [-RMaxFirst RMaxFirst (0.04 ).as(Real ) ] :Optional :RMaxFirst [/A]: Def: RMax
+ [-RMaxStep RMaxStep (0.02 ).as(Real ) ] :Optional :RMaxStep [/A]
+ [-RRMax RRMax (0.1 ).as(Real ) ] :Optional :Radial RMax [/A]
+ [-RRMaxFirst RRMaxFirst (0.04 ).as(Real ) ] :Optional :Radial RMaxFirst [/A]: Def: RMax
+ [-RRMaxStep RRMaxStep (0.02 ).as(Real ) ] :Optional :Radial RMaxStep [/A]
+ [-delBR delBR (0.0002 ).as(Real ) ] :Optional :delBR [/A]
+ [-rms rms (1e-6 ).as(Real ) ] :Optional :rms:
+ [-narrowSearch narrowSearch (1.0 ).as(Real ) ] :Optional :narrowSearch[Degree]: P-Value and Q-Value
+ [-nextTimes nextTimes (1e-4 ).as(Real ) ] :Optional :nextTimes: rms
+ [-maxIter[ation] MaxIteration (10 ).as(Integer ) ] :Optional :max iteration:
+ [-maxIter2[ation] MaxIter2 (1 ).as(Integer ) ] :Optional :max iteration on the same RMax and RRMax:
+ [-maxIter3[ation] MaxIter3 (1 ).as(Integer ) ] :Optional :max iteration on the same RMax, RRMax, and Weight:
+ [-lambda lambda (1.0 ).as(Real ) ] :Optional :labda:
+ [-ctf CTF (0 ).as(Integer ) ] :Optional :CTF Compensation
+ [-WhiteNoise WhiteNoise (0.0 ).as(Real ) ] :Optional :White Noise
+ [-below below (90.0 ).as(Real ) ] :Optional :below
+ [-noantipole ] :Optional :No Antipole
+ [-magLimit ] :Optional :magLimit
+ [-eachTime ] :Optional :each time
+ [-continue Continue (NULL ).as(inFile ) ] :Optional :continue
+ [-forContinue ForContinue (NULL ).as(outFile ) ] :Optional :For continue
+ [-phi phimin (0.0 ).as(Real )
+ phimax (360.0 ).as(Real )
+ delphi (10.0 ).as(Real ) ] :Optional :phi:[degree]
+ [-z zmin (0.0 ).as(Real )
+ zmax (30.0 ).as(Real )
+ delz (5.0 ).as(Real ) ] :Optional :z:[A]
+ [-shift shiftmin (-10.0 ).as(Real )
+ shiftmax (10.0 ).as(Real )
+ delshift (1.0 ).as(Real ) ] :Optional :shift:[A]
+ [-log Log (stdout ).as(outFile ) ] :Optional :LogFile
+ [-Normalization ] :Optional :Normalization
+ [-pvm pvm (0 ).as(Integer ) ] :Optional :pvmNumber
+ [-pvmList pvmList (NULL ).as(inFile ) ] :Optional :pvmList
+ [-pvmServer ] :Optional :Work as a server !!
+ [-pvmClient ] :Optional :Work as a client !!
+ [-wd WorkingDir (./ ).as(String ) ] :Optional :Working Directory !!
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
-m 0: The 1st version algorism(Sharing)
-m 1: The 2nd version algorism(Least Square)
<PRE>
Usage: llExtractWithLayerSeparationCtrlFileCreate
Options:
- [-i[nput] In (NULL )] :Optional :Input DataFile
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-t[urn] Turn (-13 )] :Essential :Tern
- [-u[nit] Unit (28 )] :Essential :Unit
- [-N[-helix] nHelix (1 )] :Optional :Helix
- [-dY dY (3 )] :Optional :Position of the 1st layer line: [pixel]
- [-truePitch truePitch (770 )] :Essential :truePitch [A]
- [-rMax rMax (50 )] :Essential :rMax [A]
- [-RMax RMax (0.1 )] :Optional :RMax [/A]
- [-RZMax RZMax (0.1 )] :Optional :RZMax [/A]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Optional :Input DataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-t[urn] Turn (-13 ).as(Integer ) ] :Essential :Tern
+ [-u[nit] Unit (28 ).as(Integer ) ] :Essential :Unit
+ [-N[-helix] nHelix (1 ).as(Integer ) ] :Optional :Helix
+ [-dY dY (3 ).as(Integer ) ] :Optional :Position of the 1st layer line: [pixel]
+ [-truePitch truePitch (770 ).as(Integer ) ] :Essential :truePitch [A]
+ [-rMax rMax (50 ).as(Real ) ] :Essential :rMax [A]
+ [-RMax RMax (0.1 ).as(Real ) ] :Optional :RMax [/A]
+ [-RZMax RZMax (0.1 ).as(Real ) ] :Optional :RZMax [/A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: llExtractWithLayerSeparationCtrlFileCreateMyosin
Options:
- [-i[nput] In (NULL )] :Optional :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-Y Y (6 )] :Optional :Range of Layer Line
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-Y Y (6 ).as(Real ) ] :Optional :Range of Layer Line
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: llExtractWithLayerSeparationFilamentInfo
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-o[utput] F[ile] OutF (NULL )] :Optional :OutputDataFile
- [-o[utput]I[nformation]OutI (NULL )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-truePitch truePitch (430 )] :Optional :True Pitch
- [-PixelSize PixelSize (5 )] :Optional :Pixel Size [A]
- [-deltadY deltadY (0.5 )] :Optional :A range of deltadY to determine dY.
- [-kV kV (200 )] :Optional :AccVol[kV]
- [-Cs Cs (2.1 )] :Optional :Cs[mm]
- [-df Defocus (27000 )] :Optional :Defocus[A]:under(+)
- [-A AoverP (0.1 )] :Optional :AmplitudeContrast/PhaseContrast
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-o[utput] F[ile] OutF (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-o[utput]I[nformation]OutI (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-truePitch truePitch (430 ).as(Real ) ] :Optional :True Pitch
+ [-PixelSize PixelSize (5 ).as(Real ) ] :Optional :Pixel Size [A]
+ [-deltadY deltadY (0.5 ).as(Real ) ] :Optional :A range of deltadY to determine dY.
+ [-kV kV (200 ).as(Real ) ] :Optional :AccVol[kV]
+ [-Cs Cs (2.1 ).as(Real ) ] :Optional :Cs[mm]
+ [-df Defocus (27000 ).as(Real ) ] :Optional :Defocus[A]:under(+)
+ [-A AoverP (0.1 ).as(Real ) ] :Optional :AmplitudeContrast/PhaseContrast
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: ltlg2mrc
Options:
- [-i[nput] In (NULL )] :Optional :InputDataFile
- [-o[utput] Out (NULL )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-t[itle] Title (NULL )] :Optional :Title
- [-d[elta] delta (2.5 )] :Optional :delta[A]
- [-C RepeatDistance (2.5 )] :Optional :RepeatDistance[A]
- [-r[Max] rMax (2.5 )] :Optional :rMax[A]
- [-p[hiStart] phiStart (0 )] :Optional :phiStart[degree]
- [-zmi[n] zMin (0.0 )] :Optional :zMin
- [-zma[x] zMax (55.0 )] :Optional :zMax
- [-zde[lta] deltaz (2.5 )] :Optional :deltaz
- [-w[eight] WeightOf0thLayer (0.5 )] :Optional :WeightOf0thLayer
- [-l[Weight] Layer (NULL )] :Optional :Layer WeightOfEachLayer
- [-f9[9] ] :Optional :IF(NN(LL)!=NL(LL)) WT(LL) = 0.0
- [-O[ffset] CUT (0.5 )] :Optional :CUT
- [-a[mean] Mean (0.0 )] :Optional :Mean
- [-s[igma] Sigma (0.0 )] :Optional :Sigma
- [-I[nverse] ] :Optional :Nega-Posi Reverse
- [-n[otInteractive] ] :Optional :not Intaracitve
- [-AntiPole ] :Optional :Anti Pole: zmax -> zmin: Else zmin->zmax
- [-m[ode] mode (0 )] :Optional :
+ [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-t[itle] Title (NULL ).as(String ) ] :Optional :Title
+ [-d[elta] delta (2.5 ).as(Real ) ] :Optional :delta[A]
+ [-C RepeatDistance (2.5 ).as(Real ) ] :Optional :RepeatDistance[A]
+ [-r[Max] rMax (2.5 ).as(Real ) ] :Optional :rMax[A]
+ [-p[hiStart] phiStart (0 ).as(Real ) ] :Optional :phiStart[degree]
+ [-zmi[n] zMin (0.0 ).as(Real ) ] :Optional :zMin
+ [-zma[x] zMax (55.0 ).as(Real ) ] :Optional :zMax
+ [-zde[lta] deltaz (2.5 ).as(Real ) ] :Optional :deltaz
+ [-w[eight] WeightOf0thLayer (0.5 ).as(Real ) ] :Optional :WeightOf0thLayer
+ [-l[Weight] Layer (NULL ).as(inFile ) ] :Optional :Layer WeightOfEachLayer
+ [-f9[9] ] :Optional :IF(NN(LL)!=NL(LL)) WT(LL) = 0.0
+ [-O[ffset] CUT (0.5 ).as(Real ) ] :Optional :CUT
+ [-a[mean] Mean (0.0 ).as(Real ) ] :Optional :Mean
+ [-s[igma] Sigma (0.0 ).as(Real ) ] :Optional :Sigma
+ [-I[nverse] ] :Optional :Nega-Posi Reverse
+ [-n[otInteractive] ] :Optional :not Intaracitve
+ [-AntiPole ] :Optional :Anti Pole: zmax -> zmin: Else zmin->zmax
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :
0: Normarize
1: Not Normarize bu edge average is zero.
2: Not Normarize
<PRE>
Usage: ltlgDataInfo
Options:
- [-i[nput] In ] :Essential :InputDataFile
- [-o[utput] Out ] :Optional :OutputDataFile
- [-c[onfig] configFile ] :Optional :ConfigurationFile
- [-m[ode] mode ] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- mode -----
1: Header Information
2: (N, L) Information
[-o[utput] Out (NULL ).as(outFileList::ASCII ) ] :Essential :Output:
[-o[utput]t[ype] OutType (2 ).as(Integer ) ] :Optional :Input:
[-o[utput]EA OutEA (NULL ).as(outFileList::ASCII ) ] :Essential :Output:
+ [-zero ZeroPlane (0 ).as(Integer ) ] :Optional :Zero Plane
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
<PRE>
Usage: matrix3DEulerAngleTransform
Options:
- [-i[nputlist] In (NULL )] :Essential :InputDataFileList
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-R[otationalMode] RotationalMode (ZONS )] :Optional :RotationalMode
- [-M[ultiplyEulerAngle]RotMode (ZONS )Rot1 (0.0 )Rot2 (0.0 )Rot3 (0.0 )] :Optional :M * input
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nputlist] In (NULL ).as(inFileListNoOpen ) ] :Essential :InputDataFileList
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-R[otationalMode] RotationalMode (ZONS ).as(String ) ] :Optional :RotationalMode
+ [-M[ultiplyEulerAngle]RotMode (ZONS ).as(String )
+ Rot1 (0.0 ).as(Real )
+ Rot2 (0.0 ).as(Real )
+ Rot3 (0.0 ).as(Real ) ] :Optional :M * input
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- input file format -----
filename rotationalMode phi theta psi
<PRE>
Usage: matrix3DFromEulerAngle
Options:
- [-i[nput] In (stdin )] :Optional :InputDataFile
- [-R[ot] EMode (ZONS )Rot1 (0.0 )Rot2 (0.0 )Rot3 (0.0 )] :Optional :Input: RotAngle[degree]
- [-o[utput] Out (stdout )] :Optional :Output: Matrix
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (stdin ).as(inFile ) ] :Optional :InputDataFile
+ [-R[ot] EMode (ZONS ).as(String )
+ Rot1 (0.0 ).as(Real )
+ Rot2 (0.0 ).as(Real )
+ Rot3 (0.0 ).as(Real ) ] :Optional :Input: RotAngle[degree]
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: Matrix
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: matrix3DInverse
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: matrix3DToEulerAngle
Options:
- [-i[nput] In (stdin )] :Optional :Input: Matrix3D
- [-o[utput] Out (stdout )] :Optional :Output: File
- [-E[uler]M[ngle] EulerMode (ZONS )] :Optional :Input: Mode
- [-Check Threshold (1e-4 )] :Optional :Input: Check Threshold
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (stdin ).as(inFile ) ] :Optional :Input: Matrix3D
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: File
+ [-E[uler]M[ngle] EulerMode (ZONS ).as(String ) ] :Optional :Input: Mode
+ [-Check Threshold (1e-4 ).as(Real ) ] :Optional :Input: Check Threshold
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: moi2mrc
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Optional :OutputDataFile
- [-Mag[nification] Mag (150 )] :Optional :Magnification[xk]:
- [-Mag2[nification] Mag2 (1.64 )] :Optional :Magnification[CCD/Film]
- [-ADUperE ADUperE (20 )] :Optional :[ADU/electron]
- [-info Info (1 )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (1 )] :Optional :Mode: 0:char(mean+-3sd) 1:short(direct) 2:float(e-)
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-Mag[nification] Mag (150 ).as(Real ) ] :Optional :Magnification[xk]:
+ [-Mag2[nification] Mag2 (1.64 ).as(Real ) ] :Optional :Magnification[CCD/Film]
+ [-ADUperE ADUperE (20 ).as(Real ) ] :Optional :[ADU/electron]
+ [-info Info (1 ).as(Integer ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (1 ).as(Integer ) ] :Optional :Mode: 0:char(mean+-3sd) 1:short(direct) 2:float(e-)
----- Additional Usage -----
>>>> -info Integer
1: All Header Info List
<PRE>
Usage: molecularEnvelopeResampling
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-Rmax Rmax (1.0 )] :Optional :Rmax: [/A]
- [-dR dR (0.01 )] :Optional :dR: [/A]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-Rmax Rmax (1.0 ).as(Real ) ] :Optional :Rmax: [/A]
+ [-dR dR (0.01 ).as(Real ) ] :Optional :dR: [/A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
-/bin/bash: molvie: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>molvie</TITLE>
+</HEAD>
+<BODY>
+<H1>molvie</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: molvie
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: molvieDock: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>molvieDock</TITLE>
+</HEAD>
+<BODY>
+<H1>molvieDock</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: molvieDock
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: molvieFlight: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>molvieFlight</TITLE>
+</HEAD>
+<BODY>
+<H1>molvieFlight</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: molvieFlight
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: molvieMrcViewer: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>molvieMrcViewer</TITLE>
+</HEAD>
+<BODY>
+<H1>molvieMrcViewer</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: molvieMrcViewer
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: molvieProjection: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>molvieProjection</TITLE>
+</HEAD>
+<BODY>
+<H1>molvieProjection</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: molvieProjection
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: molvieViewer: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>molvieViewer</TITLE>
+</HEAD>
+<BODY>
+<H1>molvieViewer</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: molvieViewer
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: mrc2fld
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-shiftx shiftx (0.0 )] :Optional :shiftx[A]
- [-shifty shifty (0.0 )] :Optional :shifty[A]
- [-shiftz shiftz (0.0 )] :Optional :shiftz[A]
- [-I ] :Optional :Inverse
- [-R[adius]C[ylindrical]] :Optional :Radius: Cylindrical
- [-M[ag] Mag (1.0 )] :Optional :density x mag
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-shiftx shiftx (0.0 ).as(Real ) ] :Optional :shiftx[A]
+ [-shifty shifty (0.0 ).as(Real ) ] :Optional :shifty[A]
+ [-shiftz shiftz (0.0 ).as(Real ) ] :Optional :shiftz[A]
+ [-I ] :Optional :Inverse
+ [-R[adius]C[ylindrical] ] :Optional :Radius: Cylindrical
+ [-M[ag] Mag (1.0 ).as(Real ) ] :Optional :density x mag
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
mode 0:Char(Byte) Image
If you want to use volume rendering, you must select Char.
mode 2:Float Image
<PRE>
Usage: mrc2gif
Options:
- [-i[nput] inFile (NULL )] :Essential :InputDataFile
- [-o[utput] outFile (NULL )] :Essential :OutputDataFile
- [-H[igh] High (0 )] :Optional :HighThreshold
- [-L[ow] Low (0 )] :Optional :LowThreshold
- [-I[nverse] ] :Optional :Inverse(Black is white)
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode:
+ [-i[nput] inFile (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] outFile (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-H[igh] High (0 ).as(Real ) ] :Optional :HighThreshold
+ [-L[ow] Low (0 ).as(Real ) ] :Optional :LowThreshold
+ [-I[nverse] ] :Optional :Inverse(Black is white)
+ [-z[Section] Z (0 ).as(Integer ) ] :Optional :z-section
+ [-e[xtention] format (%s.%04d ).as(String ) ] :Optional :SerialSection Format
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode:
0 (8bits), 1(16bits)
+-z
+ -1: Serial Files
+ z(>0): Section at z
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrc2map
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-noswap ] :Optional : NO Byte Swapping
- [-shiftx shiftx (0.0 )] :Optional :shiftx
- [-shifty shifty (0.0 )] :Optional :shifty
- [-shiftz shiftz (0.0 )] :Optional :shiftz
- [-mul mul (1.0 )] :Optional :mrc*mul
- [-m[ode] mode (0 )] :Optional :Mode:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-noswap ] :Optional : NO Byte Swapping
+ [-shiftx shiftx (0.0 ).as(Real ) ] :Optional :shiftx
+ [-shifty shifty (0.0 ).as(Real ) ] :Optional :shifty
+ [-shiftz shiftz (0.0 ).as(Real ) ] :Optional :shiftz
+ [-mul mul (1.0 ).as(Real ) ] :Optional :mrc*mul
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode:
0 : Same as mrc
1 : Helix(CentreIsOrigin)
2: BottomRight is Origin
<PRE>
Usage: mrc2mrc
Options:
- [-i[nput] In (NULL )] :Essential :Input:
- [-i[nput]t[ype] InType (FEIextendedMRC)] :Optional :InputDataType
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-o[utput]t[ype] OutType (Eos )] :Optional :OutputDataType
- [-Length LenX (1.0 )LenY (1.0 )LenZ (1.0 )] :Optional :Mode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input:
+ [-i[nput]t[ype] InType (FEIextendedMRC).as(String ) ] :Optional :InputDataType
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-o[utput]t[ype] OutType (Eos ).as(String ) ] :Optional :OutputDataType
+ [-Length LenX (1.0 ).as(Real )
+ LenY (1.0 ).as(Real )
+ LenZ (1.0 ).as(Real ) ] :Optional :Mode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
>> To be suppoerted (Not all)
Eos
<PRE>
Usage: mrc2tiff
Options:
- [-i[nput] inFile (NULL )] :Essential :InputDataFile
- [-o[utput] outFile (NULL )] :Essential :OutputDataFile
- [-H[igh] High (0 )] :Optional :HighThreshold
- [-L[ow] Low (0 )] :Optional :LowThreshold
- [-I[nverse] ] :Optional :Inverse(Black is white)
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode:
+ [-i[nput] inFile (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] outFile (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-H[igh] High (0 ).as(Real ) ] :Optional :HighThreshold
+ [-L[ow] Low (0 ).as(Real ) ] :Optional :LowThreshold
+ [-I[nverse] ] :Optional :Inverse(Black is white)
+ [-Z Z (0 ).as(Integer ) ] :Optional :Each: 0<=, SerialSection:-1
+ [-e[xtension] format (%s.%04d ).as(String ) ] :Optional :SerialSectionFormat
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode:
0 (8bits), 1(16bits)
--- Attention ---
<PRE>
Usage: mrc3DExtractZ
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-b[ottom] ZB (0 )] :Optional :Bottom of output data
- [-t[op] ZT (-1 )] :Optional :Top of output data. Default:top of input data
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-b[ottom] ZB (0 ).as(Integer ) ] :Optional :Bottom of output data
+ [-t[op] ZT (-1 ).as(Integer ) ] :Optional :Top of output data. Default:top of input data
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrc3Dto2D
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrcImage[3D]
- [-o[utput] Out (NULL )] :Optional :Output: mrcImage[2D]
- [-fileList filenamePrefix (2D )filenameSuffix (2d )filenameFormat (%s-%05d.%s)] :Optional :Output: mrcImage[2D] List
- [-Rot1 Rot1Start (0.0 )Rot1End (360.0 )Rot1Delta (10 )] :Optional :OutputDataFile
- [-Rot2 Rot2Start (0.0 )Rot2End (360.0 )Rot2Delta (10 )] :Optional :OutputDataFile
- [-Rot3 Rot3Start (0.0 )Rot3End (360.0 )Rot3Delta (10 )] :Optional :OutputDataFile
- [-EulerMode EulerMode (ZOYS )] :Optional :OutputDataFile
- [-InterpolationMode InterpolationMode (1 )] :Optional :OutputDataFile
- [-AreaMode AreaMode (0 )] :Optional :Cubic: 0, Globular: 1
- [-pthread pthreadMax (1 )] :Optional :pthread: max
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrcImage[3D]
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :Output: mrcImage[2D]
+ [-fileList filenamePrefix (2D ).as(String )
+ filenameSuffix (2d ).as(String )
+ filenameFormat (%s-%05d.%s).as(String ) ] :Optional :Output: mrcImage[2D] List
+ [-Rot1 Rot1Start (0.0 ).as(Real )
+ Rot1End (360.0 ).as(Real )
+ Rot1Delta (10 ).as(Real ) ] :Optional :OutputDataFile
+ [-Rot2 Rot2Start (0.0 ).as(Real )
+ Rot2End (360.0 ).as(Real )
+ Rot2Delta (10 ).as(Real ) ] :Optional :OutputDataFile
+ [-Rot3 Rot3Start (0.0 ).as(Real )
+ Rot3End (360.0 ).as(Real )
+ Rot3Delta (10 ).as(Real ) ] :Optional :OutputDataFile
+ [-EulerMode EulerMode (ZOYS ).as(String ) ] :Optional :OutputDataFile
+ [-InterpolationMode InterpolationMode (1 ).as(Integer ) ] :Optional :OutputDataFile
+ [-AreaMode AreaMode (0 ).as(Integer ) ] :Optional :Cubic: 0, Globular: 1
+ [-pthread pthreadMax (1 ).as(Integer ) ] :Optional :pthread: max
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- Attention !!!! -----
-m 0:
<PRE>
Usage: mrcFETnormalizeBySD
Options:
- [-i[nput] In (NULL )] :Essential :InputFileList
- [-i[nput]s[ample] InSample (NULL )] :Optional :FileListforSDcalc
- [-r[ead]SD readSD (NULL )] :Optional :readFETSDfile
- [-w[rite]SD writeSD (NULL )] :Optional :writeFETSDfile
- [-o[utput] Out (NULL )] :Optional :OutputASmrcImage
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputFileList
+ [-i[nput]s[ample] InSample (NULL ).as(inFile ) ] :Optional :FileListforSDcalc
+ [-r[ead]SD readSD (NULL ).as(inFile ) ] :Optional :readFETSDfile
+ [-w[rite]SD writeSD (NULL ).as(outFile ) ] :Optional :writeFETSDfile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputASmrcImage
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
-is :[inputsample] is FileList for SDcalculation.
<PRE>
Usage: mrcFFTBandPassFilter
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcFFTCTFCompensation
Options:
- [-i[nput] In ] :Essential :InputDataFile
- [-o[utput] Out ] :Essential :OutputDataFile
- [-I[nputWeight] CTFIn ] :Essential :InputWeightFile
- [-c[onfig] configFile ] :Optional :ConfigurationFile
- [-m[ode] mode ] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-I[nputWeight] CTFIn (NULL ).as(inFile ) ] :Essential :InputWeightFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
>>> CTFWeigting File
RR0 F0 : If R<RR0, Weight=0. If RR0<=R<RR1, Weight={(RR1-R)*F0+(R-RR0)*F1}/(RR1-RR0), i.e., Linear Interpolation
RR1 F1 :
<PRE>
Usage: mrcFFTDigitize
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-l[evel] Level (2.0 )] :Optional :Level
- [-min[imum] Min (0.0 )] :Essential :Minimum
- [-max[imum] Max (0.0 )] :Essential :Maximum
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-l[evel] Level (2.0 ).as(Real ) ] :Optional :Level
+ [-min[imum] Min (0.0 ).as(Real ) ] :Essential :Minimum
+ [-max[imum] Max (0.0 ).as(Real ) ] :Essential :Maximum
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcFFTExpression
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-T[hreshold] Thres (1e-16 )] :Optional :Threshold to calculate.For mode 1 and 3.
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-T[hreshold] Thres (1e-16 ).as(Real ) ] :Optional :Threshold to calculate.For mode 1 and 3.
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- FFT Expression MOde -----
0:Amplitude
<PRE>
Usage: mrcFFTFibreDiagram
Options:
- [-i[nput] In (NULL )] :Essential :Input: HelicalObject/FFT3D or Image3D
- [-o[utput] Out (NULL )] :Essential :Output: 2D mrcImage
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: HelicalObject/FFT3D or Image3D
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: 2D mrcImage
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
-mode 0 : average PHI-axis to express RZ space
</PRE>
<PRE>
Usage: mrcFFTFiltering
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :Output: Filtered Image
- [-IQ IQ (NULL )] :Optional :Output: IQ Map
- [-vx vx (0 )] :Optional :Vector(x)
- [-vy vy (0 )] :Optional :Vector(y)
- [-v1 v1x (0 )v1y (0 )] :Optional :Vector(v1)
- [-v2 v2x (0 )v2y (0 )] :Optional :Vector(v2)
- [-sx sx (1 )] :Optional :Size(x)
- [-sy sy (1 )] :Optional :Size(y)
- [-neg[lect]F00 ] :Optional :Neglect F00
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: Filtered Image
+ [-IQ IQ (NULL ).as(outFile ) ] :Optional :Output: IQ Map
+ [-vx vx (0 ).as(Real ) ] :Optional :Vector(x)
+ [-vy vy (0 ).as(Real ) ] :Optional :Vector(y)
+ [-v1 v1x (0 ).as(Real )
+ v1y (0 ).as(Real ) ] :Optional :Vector(v1)
+ [-v2 v2x (0 ).as(Real )
+ v2y (0 ).as(Real ) ] :Optional :Vector(v2)
+ [-sx sx (1 ).as(Integer ) ] :Optional :Size(x)
+ [-sy sy (1 ).as(Integer ) ] :Optional :Size(y)
+ [-neg[lect]F00 ] :Optional :Neglect F00
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcFFTIQEstimation
Options:
- [-i[nput] In (NULL )] :Essential :Input: MRC
- [-sp[otList] SpotList (stdin )] :Essential :Input: SpotList: X Y Z
- [-radius radius (3 )] :Optional :Input: [pixel]
- [-o[utput] Out (NULL )] :Essential :Output: ASCII
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: MRC
+ [-sp[otList] SpotList (stdin ).as(inFile ) ] :Essential :Input: SpotList: X Y Z
+ [-radius radius (3 ).as(Integer ) ] :Optional :Input: [pixel]
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: ASCII
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcFFTLayerLineCheck
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrc(FT)
- [-L[ayer] L (2 )] :Optional :Input: Layer(pixel)
- [-NoEq ] :Optional :Input: No l=0
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrc(FT)
+ [-L[ayer] L (2 ).as(Integer ) ] :Optional :Input: Layer(pixel)
+ [-NoEq ] :Optional :Input: No l=0
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcFFTMedianFilter
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-r r (1 )] :Optional :Radius of Kernel Size (Pixel)
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-r r (1 ).as(Real ) ] :Optional :Radius of Kernel Size (Pixel)
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
Calculation is performed on amplitude only.
Output: Real part is amplitude and imaginary part is zero.
<PRE>
Usage: mrcFFTProjection
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
The 2D FFT Image projects to Y-axis
This image is not true.
<PRE>
Usage: mrcFFTResampling
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-nx[umber] Nx (64.0 )] :Optional :NumberX
- [-ny[umber] Ny (64.0 )] :Optional :NumberY
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-nx[umber] Nx (64.0 ).as(Real ) ] :Optional :NumberX
+ [-ny[umber] Ny (64.0 ).as(Real ) ] :Optional :NumberY
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcFFTShellInfo
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrc/FFT
- [-o[utput] Out (stdout )] :Optional :Output:
- [-R[angeOfShell] minR (0 )maxR (0.1 )] :Optional :minR/maxR[/A]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (1 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrc/FFT
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output:
+ [-R[angeOfShell] minR (0 ).as(Real )
+ maxR (0.1 ).as(Real ) ] :Optional :minR/maxR[/A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (1 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
-mode 1 : AveragedMagnitute
-mode 2 : AveragedPower
<PRE>
Usage: mrcFFTSizeChange
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-x[length] Nx (1.0 )] :Optional :Pixel size
- [-y[length] Ny (1.0 )] :Optional :Pixel size
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-x[length] Nx (1.0 ).as(Real ) ] :Optional :Pixel size
+ [-y[length] Ny (1.0 ).as(Real ) ] :Optional :Pixel size
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcFFTSpectrum
Options:
- [-i[nput] In (NULL )] :Essential :Input:fft
- [-o[utput] Out (stdout )] :Optional :Output:spectrum
- [-n N (1 )] :Optional :n-division: 2PI/n
- [-axis Axis (0.0 )] :Optional :axis: 0
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input:fft
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output:spectrum
+ [-n N (1 ).as(Integer ) ] :Optional :n-division: 2PI/n
+ [-axis Axis (0.0 ).as(Real ) ] :Optional :axis: 0
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcFFTXFiltering
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-RMaxX RMaxX (0 )] :Optional :RMax value of X [1/A]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-RMaxX RMaxX (0 ).as(Real ) ] :Optional :RMax value of X [1/A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
This filter cuts high resolution information only X direction.
RMaxX [1/A] is maximum resolution
<PRE>
Usage: mrcFFTplainreduce
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-p[osition] Pos (0 )] :Optional :Position of reduced plain
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-v[alue] Value (0 )] :Optional :Value to multiply
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-p[osition] Pos (0 ).as(Integer ) ] :Optional :Position of reduced plain
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-v[alue] Value (0 ).as(Real ) ] :Optional :Value to multiply
----- Additional Usage -----
mode 0:pos=z.
mode 1:pos=x.
<PRE>
Usage: mrcFTMeridianEquatorRedece
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-X MaxX (-1 )] :Optional :Max X to put zero (pixel). Default is no operation.
- [-Y MaxY (-1 )] :Optional :Max Y to put zero (pixel). Default is no operation.
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-X MaxX (-1 ).as(Integer ) ] :Optional :Max X to put zero (pixel). Default is no operation.
+ [-Y MaxY (-1 ).as(Integer ) ] :Optional :Max Y to put zero (pixel). Default is no operation.
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImage1DProjectionfrom2D
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-d[egree] phi (0 )] :Optional :Degree of the line to project
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-d[egree] phi (0 ).as(Real ) ] :Optional :Degree of the line to project
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImage1dAverageByCorrelation
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-r[ange] range (0 )] :Optional :Search range of shift.Default:Nx
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-r[eference] Ref (NULL ).as(inFile ) ] :Essential :ReferenceDataFile
+ [-range range (0 ).as(Integer ) ] :Optional :Search range of shift.Default:Nx
+ [-s[ignal position] Signal (NULL ).as(inFile ) ] :Essential :File to define position of signal
+ [-d[elta] delta (1.0 ).as(Real ) ] :Optional :Spacing of molecule(Pixel).
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImage1dShiftAverageByAnnealing
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-s[ignal position] Signal (NULL )] :Essential :File to define position of signal
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-r[ange] range (0 )] :Optional :Search range of shift.Default:Nx
- [-d[elta] delta (1.0 )] :Optional :Spacing of molecule(Pixel).
- [-T[eperature] temperature (1.0 )] :Optional :Initial temperature.
- [-iter[ation] iter (1000 )] :Optional :Number of iteration before reducing temperature.
- [-eps[ilon] eps (0.001 )] :Optional :Temperature(T) reduced to (1-epsilon)T.
- [-tol tol (1e-2 )] :Optional :Number to identify convergence
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-M[ode2] mode2 (0 )] :Optional :Mode2
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-s[ignal position] Signal (NULL ).as(inFile ) ] :Essential :File to define position of signal
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-r[ange] range (0 ).as(Integer ) ] :Optional :Search range of shift.Default:Nx
+ [-d[elta] delta (1.0 ).as(Real ) ] :Optional :Spacing of molecule(Pixel).
+ [-T[eperature] temperature (1.0 ).as(Real ) ] :Optional :Initial temperature.
+ [-iter[ation] iter (1000 ).as(Integer ) ] :Optional :Number of iteration before reducing temperature.
+ [-eps[ilon] eps (0.001 ).as(Real ) ] :Optional :Temperature(T) reduced to (1-epsilon)T.
+ [-tol tol (1e-2 ).as(Real ) ] :Optional :Number to identify convergence
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-M[ode2] mode2 (0 ).as(Integer ) ] :Optional :Mode2
----- mode -----
0:All search
1:annealing method
<PRE>
Usage: mrcImage1dShiftByCorrelation
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-r[eference] Ref (NULL )] :Essential :ReferenceDataFile
- [-range range (0 )] :Optional :Search range of shift.Default:Nx
- [-s[ignal position] Signal (NULL )] :Essential :File to define position of signal
- [-d[elta] delta (1.0 )] :Optional :Spacing of molecule(Pixel).
- [-norm[alize] ] :Optional :Normalize before correlation
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-r[eference] Ref (NULL ).as(inFile ) ] :Essential :ReferenceDataFile
+ [-range range (0 ).as(Integer ) ] :Optional :Search range of shift.Default:Nx
+ [-s[ignal position] Signal (NULL ).as(inFile ) ] :Essential :File to define position of signal
+ [-d[elta] delta (1.0 ).as(Real ) ] :Optional :Spacing of molecule(Pixel).
+ [-norm[alize] ] :Optional :Normalize before correlation
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- mode -----
0:Phase residual
<PRE>
Usage: mrcImage2DBackProjection
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-z NumZ (10 )] :Optional :Z: pixel
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-z NumZ (10 ).as(Integer ) ] :Optional :Z: pixel
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImage2DProjection
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-w[omega] Omega (0 )] :Optional :Omega
- [-p[hi] Phi (0 )] :Optional :Phi
- [-a[lpha] Alpha (0 )] :Optional :Alpha
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-w[omega] Omega (0 ).as(Real ) ] :Optional :Omega
+ [-p[hi] Phi (0 ).as(Real ) ] :Optional :Phi
+ [-a[lpha] Alpha (0 ).as(Real ) ] :Optional :Alpha
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImage2pdb
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (5 )] :Optional :Mode
- [-hi[gh] h (0 )] :Optional :Value of high threshold. Default is the MAX.
- [-lo[w] l (0 )] :Optional :Value of low threshold. Default is the MIN.
- [-L[attice] ] :Optional :Atoms are on lattice points
- [-Skip Skip (1 )] :Optional :Skip atoms.
- [-R[andom] Random (0 )] :Optional :Random
- [-d[elta] delta (0.1 )] :Optional :Delta to select atoms to avoid too much concentration. Requiers 0-0.5 value. For mode2-4.
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (5 ).as(Integer ) ] :Optional :Mode
+ [-hi[gh] h (0 ).as(Real ) ] :Optional :Value of high threshold. Default is the MAX.
+ [-lo[w] l (0 ).as(Real ) ] :Optional :Value of low threshold. Default is the MIN.
+ [-L[attice] ] :Optional :Atoms are on lattice points
+ [-Skip Skip (1 ).as(Integer ) ] :Optional :Skip atoms.
+ [-R[andom] Random (0 ).as(Real ) ] :Optional :Random
+ [-d[elta] delta (0.1 ).as(Real ) ] :Optional :Delta to select atoms to avoid too much concentration. Requiers 0-0.5 value. For mode2-4.
----- Additional Usage -----
mode0: One atom for one boxel.
mode1: Eight atoms for one boxel.
<PRE>
Usage: mrcImage3DHighResoEmphasis
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-L[owThreshold] L (0 )] :Optional :Low threshold to modify
- [-H[ighThreshold] H (0 )] :Optional :High threshold to modify
- [-A[value] A (0 )] :Optional :A value
- [-B[value] B (0 )] :Optional :B value
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-L[owThreshold] L (0 ).as(Real ) ] :Optional :Low threshold to modify
+ [-H[ighThreshold] H (0 ).as(Real ) ] :Optional :High threshold to modify
+ [-A[value] A (0 ).as(Real ) ] :Optional :A value
+ [-B[value] B (0 ).as(Real ) ] :Optional :B value
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- algorithm -----
R<L data*exp(A*L+B*L*L)
L<R<H data*exp(A*R+B*R*R)
<PRE>
Usage: mrcImage3DPad
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-r[max] r (0 )] :Optional :Threshold radius of signal.Default is Nx.
- [-w[idth] w (1 )] :Optional :Width of slope. For mode 1.
- [-v[alue] v (0 )] :Optional :Value of out of threshold.
- [-Nx Nx (0 )] :Optional :Number of x.Default is inputfile.
- [-Ny Ny (0 )] :Optional :Number of y.Default is inputfile.
- [-Nz Nz (0 )] :Optional :Number of z.Default is inputfile.
- [-Floating ] :Optional :Floating
- [-m[ode] mode (0 )] :Optional :Mode
- [-M[ode2] mode2 (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-r[max] r (0 ).as(Real ) ] :Optional :Threshold radius of signal.Default is Nx.
+ [-w[idth] w (1 ).as(Real ) ] :Optional :Width of slope. For mode 1.
+ [-v[alue] v (0 ).as(Real ) ] :Optional :Value of out of threshold.
+ [-Nx Nx (0 ).as(Integer ) ] :Optional :Number of x.Default is inputfile.
+ [-Ny Ny (0 ).as(Integer ) ] :Optional :Number of y.Default is inputfile.
+ [-Nz Nz (0 ).as(Integer ) ] :Optional :Number of z.Default is inputfile.
+ [-Floating ] :Optional :Floating
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-M[ode2] mode2 (0 ).as(Integer ) ] :Optional :Mode
----- mode -----
0:Default: Out of threshold is avrage of threshold plain.
1:Mulplying cos function. Default: Out of threshold is avrage of threshold plain.
<PRE>
Usage: mrcImage3DPad2
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-r[max] r (0 )] :Optional :Threshold radius of signal.Default is Nx.
- [-w[idth] w (1 )] :Optional :Width of slope. For mode 1.
- [-v[alue] v (0 )] :Optional :Value of out of threshold.
- [-Nx Nx (0 )] :Optional :Number of x.Default is inputfile.
- [-Ny Ny (0 )] :Optional :Number of y.Default is inputfile.
- [-Nz Nz (0 )] :Optional :Number of z.Default is inputfile.
- [-Floating ] :Optional :Floating
- [-m[ode] mode (0 )] :Optional :Mode
- [-M[ode2] mode2 (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-r[max] r (0 ).as(Real ) ] :Optional :Threshold radius of signal.Default is Nx.
+ [-w[idth] w (1 ).as(Real ) ] :Optional :Width of slope. For mode 1.
+ [-v[alue] v (0 ).as(Real ) ] :Optional :Value of out of threshold.
+ [-Nx Nx (0 ).as(Integer ) ] :Optional :Number of x.Default is inputfile.
+ [-Ny Ny (0 ).as(Integer ) ] :Optional :Number of y.Default is inputfile.
+ [-Nz Nz (0 ).as(Integer ) ] :Optional :Number of z.Default is inputfile.
+ [-Floating ] :Optional :Floating
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-M[ode2] mode2 (0 ).as(Integer ) ] :Optional :Mode
----- mode -----
0:Default: Out of threshold is avrage of threshold plain.
1:Mulplying cos function. Default: Out of threshold is avrage of threshold plain.
--- /dev/null
+/bin/bash: mrcImage3DPeakGet: そのようなファイルやディレクトリはありません
<PRE>
Usage: mrcImage3DSymmetryFind
Options:
- [-i[nput] In (NULL )] :Essential :Input: MRC(3D)
- [-o[utput] Out (stdout )] :Optional :Output: SymmetryFindParameters
- [-a[verage] Avg (NULL )] :Optional :Output: SymmetryAverage
- [-S[paceGroupNumber] ISGN (0 )] :Optional :SpaceGroupNumber
- [-Rot[ation]Mode RotMode (XOYS )] :Optional :EulerMode
- [-Rot1 minRot1 (0. )maxRot1 (360. )dRot1 (1.0 )] :Optional :[degree]
- [-Rot2 minRot2 (-90. )maxRot2 (90. )dRot2 (1.0 )] :Optional :[degree]
- [-dCos dCos (1 )] :Optional :dCos
- [-CorMode corMode (16 )] :Optional :CorrelationMode
- [-OffsetMode OffsetMode (0 )] :Optional :OffsetMode
- [-InterpolationMode InterpolationMode (2 )] :Optional :InterpolationMode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: MRC(3D)
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: SymmetryFindParameters
+ [-a[verage] Avg (NULL ).as(outFile ) ] :Optional :Output: SymmetryAverage
+ [-S[paceGroupNumber] ISGN (0 ).as(Integer ) ] :Optional :SpaceGroupNumber
+ [-Rot[ation]Mode RotMode (XOYS ).as(String ) ] :Optional :EulerMode
+ [-Rot1 minRot1 (0. ).as(Real )
+ maxRot1 (360. ).as(Real )
+ dRot1 (1.0 ).as(Real ) ] :Optional :[degree]
+ [-Rot2 minRot2 (-90. ).as(Real )
+ maxRot2 (90. ).as(Real )
+ dRot2 (1.0 ).as(Real ) ] :Optional :[degree]
+ [-dCos dCos (1 ).as(Integer ) ] :Optional :dCos
+ [-CorMode corMode (16 ).as(Integer ) ] :Optional :CorrelationMode
+ [-OffsetMode OffsetMode (0 ).as(Integer ) ] :Optional :OffsetMode
+ [-InterpolationMode InterpolationMode (2 ).as(Integer ) ] :Optional :InterpolationMode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImage3DWindowing
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrcImage
- [-o[utput] Out (NULL )] :Essential :Output: mrcImage
- [-center cx (0 )cy (0 )cz (0 )] :Optional :Center:
- [-w[idth] wx (0 )wy (0 )wz (0 )] :Optional :Width
- [-r[dius] r (0 )] :Optional :Radius
- [-w[idth]r[dius] w (0 )] :Optional :Width for R
- [-w[idth]z widthz (0 )] :Optional :Width for z
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrcImage
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: mrcImage
+ [-center cx (0 ).as(Real )
+ cy (0 ).as(Real )
+ cz (0 ).as(Real ) ] :Optional :Center:
+ [-w[idth] wx (0 ).as(Real )
+ wy (0 ).as(Real )
+ wz (0 ).as(Real ) ] :Optional :Width
+ [-r[dius] r (0 ).as(Real ) ] :Optional :Radius
+ [-w[idth]r[dius] w (0 ).as(Real ) ] :Optional :Width for R
+ [-w[idth]z widthz (0 ).as(Real ) ] :Optional :Width for z
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
0: GaussianRectangularSolid
1: CosCylindar(+Offset)
<PRE>
Usage: mrcImageAbnormalValueRemove
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrc
- [-o[utput] Out (NULL )] :Essential :Output: mrc
- [-v[alueForCut] cutValue (3.0 )] :Optional :CutValue/Sigma
- [-u[nsigned] UnsignedMax (65535 )UnsignedHalf (16384 )] :Optional :Unsigned to Signed: Need Max
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrc
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: mrc
+ [-v[alueForCut] cutValue (3.0 ).as(Real ) ] :Optional :CutValue/Sigma
+ [-u[nsigned] UnsignedMax (65535 ).as(Real )
+ UnsignedHalf (16384 ).as(Real ) ] :Optional :Unsigned to Signed: Need Max
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- Mode:
0: Random Value
<PRE>
Usage: mrcImageActinSingleParticleAnalysis
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageAdaptiveBinalization
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-s[ize] Size (10 )] :Optional :Size of area to average
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-s[ize] Size (10 ).as(Integer ) ] :Optional :Size of area to average
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageAdd
Options:
- [-i1[input1] In1 (NULL )] :Optional :InputDataFile1
- [-i2[input2] In2 (NULL )] :Optional :InputDataFile2
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-I[nput array of file]In (stdin )] :Optional :InputDataFiles
+ [-i1[input1] In1 (NULL ).as(inFile ) ] :Optional :InputDataFile1
+ [-i2[input2] In2 (NULL ).as(inFile ) ] :Optional :InputDataFile2
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-I[nput array of file]In (stdin ).as(inFileListNoOpen ) ] :Optional :InputDataFiles
----- Additional Usage -----
mode 0:Add
mode 1:Add / (Number of Pictures)
<PRE>
Usage: mrcImageAddValue
Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrc
- [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: mrc
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input: mrc
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output: mrc
[-v[alue] Value (0.0 ).as(Real ) ] :Optional :Value: o=i+v
[-cuda cudaDeviceID (0 ).as(Integer ) ] :Optional :UseCuda
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
<PRE>
Usage: mrcImageAreaCalc
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrcImage
- [-o[utput] Out (NULL )] :Essential :Output: mrcImage:area
- [-O[utput] OutInfo (stdout )] :Optional :Output: ASCII: area info
- [-l[abel] Label (NULL )] :Optional :Output: mrcImage:labeling
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input: mrcImage
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output: mrcImage:area
+ [-O[utput] OutInfo (stdout ).as(outFile::ASCII ) ] :Optional :Output: ASCII: area info
+ [-l[abel] Label (NULL ).as(outFile::mrcImage ) ] :Optional :Output: mrcImage:labeling
+ [-O[utput]H[istgram] OutHist (NULL ).as(outFile::ASCII ) ] :Optional :Output: ASCII: area info
+ [-H[istgram] DelHist (1 ).as(Real ) ] :Optional :Delta
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageAssignedToTFofPDB
Options:
- [-i[nput] In ] :Essential :InputDataFile(mrcImage)
- [-p[dbFile] InPDB ] :Essential :InputDataFile(pdbFile)
- [-o[utput] Out ] :Essential :OutputDataFile(pdbFile)
- [-H[igh] HighLevel ] :Optional :HighLevel
- [-L[ow] LowLevel ] :Optional :LowLevel
- [-c[onfig] configFile ] :Optional :ConfigurationFile
- [-m[ode] mode ] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile(mrcImage)
+ [-p[dbFile] InPDB (NULL ).as(inFile ) ] :Essential :InputDataFile(pdbFile)
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile(pdbFile)
+ [-H[igh] HighLevel (0.0 ).as(Real ) ] :Optional :HighLevel
+ [-L[ow] LowLevel (-1.0 ).as(Real ) ] :Optional :LowLevel
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
>>> Mode:
0: Default.
1 : Origin is Center (1) or BottomLeft (0).
<PRE>
Usage: mrcImageAutoCorrelationWithWindowing
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-O[utput] OutWin (NULL )] :Optional :Output WindowedFile
- [-W[indowing]y Wy (6 )] :Optional :Window Height: N.y * 1/Wy
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output
+ [-o[utput]c[entre] OutCentre (NULL ).as(outFile::mrcImage ) ] :Optional :OutputDataFile
+ [-O[utput] OutWin (NULL ).as(outFile::mrcImage ) ] :Optional :Output WindowedFile
+ [-W[indowing]y Wy (6 ).as(Real ) ] :Optional :Window Height: N.y * 1/Wy
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageAutoFilamentExtract
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-i[nput]S[ource]fileInS (NULL )] :Essential :InputSourceFile
- [-o[utput]E[xtract] OutE (NULL )] :Essential :OutputFileForExtraction
- [-o[utput] Out (stdout )] :Optional :Output Log File
- [-o[utput]F[inal] OutF (stdout )] :Optional :OutputFinalFile
- [-r[oi]ROI blx (0.0 )bly (0.0 )brx (0.0 )bry (0.0 )trx (0.0 )try (0.0 )tlx (0.0 )tly (0.0 )] :Optional :Rectangle ROI
- [-r[oi]Unbent roiLine (0.0 )... ] :Variable :
- [-x x (120 )] :Optional :x range for ROI or Unbent
- [-d[elta]dYmax ddYmax (0.9 )] :Optional :delta dY max
- [-d[elta]dYmin ddYmin (0.2 )] :Optional :delta dY mim
- [-T[ransepose] T (0 )] :Optional :corresponding to mrcImageTransepose mode
- [-maxd[elta]Y maxdY (12 )] :Optional :Maximum number of layer line
- [-H[eight] R[ange] HeightRange (0 )] :Optional :Height Range [Pixel]
- [-RMaxX RMaxX (0.05 )] :Optional :RMaxX [1/A] (supported mode 1)
- [-mag mag (1.1 )] :Optional :magnification ratio
- [-truePitch truePitch (430 )] :Optional :True Pitch [A]
- [-PixelSize PixelSize (5 )] :Optional :Pixel Size [A]
- [-finaly finaly (0 )] :Optional :final y [pixel] for extraction
- [-Ignore Ignore (0 )] :Optional :Ignore the final y
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i[nput]S[ource]fileInS (NULL ).as(inFile ) ] :Essential :InputSourceFile
+ [-o[utput]E[xtract] OutE (NULL ).as(inFile ) ] :Essential :OutputFileForExtraction
+ [-o[utput] Out (stdout ).as(appendFile ) ] :Optional :Output Log File
+ [-o[utput]F[inal] OutF (stdout ).as(outFile ) ] :Optional :OutputFinalFile
+ [-r[oi]ROI blx (0.0 ).as(Real )
+ bly (0.0 ).as(Real )
+ brx (0.0 ).as(Real )
+ bry (0.0 ).as(Real )
+ trx (0.0 ).as(Real )
+ try (0.0 ).as(Real )
+ tlx (0.0 ).as(Real )
+ tly (0.0 ).as(Real ) ] :Optional :Rectangle ROI
+ [-r[oi]Unbent roiLine (0.0 ).as(Real ) ... ] :Variable :
+ [-x x (120 ).as(Real ) ] :Optional :x range for ROI or Unbent
+ [-d[elta]dYmax ddYmax (0.9 ).as(Real ) ] :Optional :delta dY max
+ [-d[elta]dYmin ddYmin (0.2 ).as(Real ) ] :Optional :delta dY mim
+ [-T[ransepose] T (0 ).as(Integer ) ] :Optional :corresponding to mrcImageTransepose mode
+ [-maxd[elta]Y maxdY (12 ).as(Integer ) ] :Optional :Maximum number of layer line
+ [-H[eight] R[ange] HeightRange (0 ).as(Integer ) ] :Optional :Height Range [Pixel]
+ [-RMaxX RMaxX (0.05 ).as(Real ) ] :Optional :RMaxX [1/A] (supported mode 1)
+ [-mag mag (1.1 ).as(Real ) ] :Optional :magnification ratio
+ [-truePitch truePitch (430 ).as(Real ) ] :Optional :True Pitch [A]
+ [-PixelSize PixelSize (5 ).as(Real ) ] :Optional :Pixel Size [A]
+ [-finaly finaly (0 ).as(Integer ) ] :Optional :final y [pixel] for extraction
+ [-Ignore Ignore (0 ).as(Integer ) ] :Optional :Ignore the final y
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- mode -----
0 : Meridian Reflection
<PRE>
Usage: mrcImageAutoFilamentExtractResultAnalysis
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-truePitch truePitch (430 )] :Optional :True Pitch
- [-PixelSize PixelSize (5 )] :Optional :Pixel Size [A]
- [-deltadY deltadY (0.5 )] :Optional :A range of deltadY to determine dY.
- [-y y (0 )] :Optional :y [pixel] for final extraction
- [-Mag mag (1.1 )] :Optional :magnification ratio
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-truePitch truePitch (430 ).as(Real ) ] :Optional :True Pitch
+ [-PixelSize PixelSize (5 ).as(Real ) ] :Optional :Pixel Size [A]
+ [-deltadY deltadY (0.5 ).as(Real ) ] :Optional :A range of deltadY to determine dY.
+ [-y y (0 ).as(Integer ) ] :Optional :y [pixel] for final extraction
+ [-Mag mag (1.1 ).as(Real ) ] :Optional :magnification ratio
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageAutoRotationCorrelation
Options:
- [-i[nput] In (NULL )] :Essential :Input: testImage [mrcImage]
- [-r[eference] Ref (NULL )] :Essential :Input: refImage [mrcImage]
- [-nRot1 nRot1 (1 )] :Optional :Rotation number of Ref for Rot1: Def 1
- [-nRot2 nRot2 (1 )] :Optional :Rotation number of Ref for Rot2: Def 1
- [-nRot3 nRot3 (1 )] :Optional :Rotation number of Ref for Rot3: Def 1
- [-dRot1 dRot1 (1.0 )] :Optional :Delta Angle [Degree] of Ref for Rot1; Def.: 360/nRot1
- [-dRot2 dRot2 (1.0 )] :Optional :Delta Angle [Degree] of Ref for Rot2; Def.: 360/nRot2
- [-dRot3 dRot3 (1.0 )] :Optional :Delta Angle [Degree] of Ref for Rot3; Def.: 360/nRot3
- [-startRot1 startRot1 (0.0 )] :Optional :Start Angle [Degree] of Ref for Rot1; Def.: 0
- [-startRot2 startRot2 (0.0 )] :Optional :Start Angle [Degree] of Ref for Rot2; Def.: 0
- [-startRot3 startRot3 (0.0 )] :Optional :Start Angle [Degree] of Ref for Rot3; Def.: 0
- [-StackOrder StackOrder (0 )] :Optional :Stack Order for Stacked 2D of references, refer to attention
- [-o[utput] Out (NULL )] :Optional :Output: Parameter [mrcImage-format]
- [-O[utput] OutASC (stdout )] :Optional :Output: Parameter [ASCII]
- [-cor[relation] corFile (NULL )] :Optional :Correation Map at Maximum (Linear) [mrcImage-format]
- [-cor[relation]2 corFile2 (NULL )] :Optional :Correation Map2 at Maximum (Set Mode Correlation)[mrcImage-format]
- [-cor[relation]All corAllFile (NULL )] :Optional :Correation Map with All Rotation [mrcImage-format]
- [-fit[tedToRef] fitFile (NULL )] :Optional :Output: rotatedImage at Maximum(Linear Correlation) [mrcImage]
- [-fit[tedToRef]2 fitFile2 (NULL )] :Optional :Output: rotatedImage at Maximum(Set Correlation mode) [mrcImage]
- [-RefineMode RefineMode (0 )] :Optional :RefinementStep: Linear:0 or SetMode:1
- [-n[umber] Rot (36 )] :Optional :Input: Rotation around the vertical axis against image plane: dRot = 360/n [degree]
- [-range minAngle (-5.0 )maxAngle (5.0 )] :Optional :Input: SearchRange: Rotation around the vertical axis against image plane
- [-refStep1 refStep1 (1 )] :Optional :SearchStep for Ref: Each Image along Rot1
- [-refStep2 refStep2 (1 )] :Optional :SearchStep for Ref: Each Image along Rot2
- [-refStep3 refStep3 (1 )] :Optional :SearchStep for Ref: Each Image along Rot3
- [-nRot1Area nRot1AreaMin (-360 )nRot1AreaMax (360 )nRot1AreaStep (25 )] :Optional :number of Ref for Rot1
- [-nRot2Area nRot2AreaMin (-360 )nRot2AreaMax (360 )nRot2AreaStep (25 )] :Optional :number of Ref for Rot2
- [-nRot3Area nRot3AreaMin (-360 )nRot3AreaMax (360 )nRot3AreaStep (25 )] :Optional :number of Ref for Rot3
- [-Iter[ation] Iter (1 )] :Optional :Iteration for Rotation around the vertical axis against image plane
- [-Method Method (0 )] :Optional :0: Correlation, 1: SSDA
- [-s[earchRegion] sminx (0 )sminy (0 )smaxx (0/*N.x-1*/)smaxy (0/*N.y-1*/)] :Optional :SearchRegion [pixel]: used in lmrcImageAutoRotationCorrelation
- [-Shift ] :Optional :Image Shift, when in > ref
- [-RepeatX RepeatX (27.3 )] :Optional :RepeatX[A]
- [-RepeatXDelta RepeatXDelta (5 )] :Optional :RepeatXDelta[A]
- [-RepeatY RepeatY (27.3 )] :Optional :RepeatY[A]
- [-RepeatYDelta RepeatYDelta (5 )] :Optional :RepeatYDelta[A]
- [-Xshift ] :Optional :X-Shift Only
- [-NoShift ] :Optional :No-Shift
- [-Log Log (stdout )] :Optional :Output: LogFile
- [-pvm pvm (1 )] :Optional :Task Number
- [-pvmList pvmList (NULL )] :Optional :ConfigurationFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: testImage [mrcImage]
+ [-r[eference] Ref (NULL ).as(inFile ) ] :Essential :Input: refImage [mrcImage]
+ [-nRot1 nRot1 (1 ).as(Integer ) ] :Optional :Rotation number of Ref for Rot1: Def 1
+ [-nRot2 nRot2 (1 ).as(Integer ) ] :Optional :Rotation number of Ref for Rot2: Def 1
+ [-nRot3 nRot3 (1 ).as(Integer ) ] :Optional :Rotation number of Ref for Rot3: Def 1
+ [-dRot1 dRot1 (1.0 ).as(Real ) ] :Optional :Delta Angle [Degree] of Ref for Rot1; Def.: 360/nRot1
+ [-dRot2 dRot2 (1.0 ).as(Real ) ] :Optional :Delta Angle [Degree] of Ref for Rot2; Def.: 360/nRot2
+ [-dRot3 dRot3 (1.0 ).as(Real ) ] :Optional :Delta Angle [Degree] of Ref for Rot3; Def.: 360/nRot3
+ [-startRot1 startRot1 (0.0 ).as(Real ) ] :Optional :Start Angle [Degree] of Ref for Rot1; Def.: 0
+ [-startRot2 startRot2 (0.0 ).as(Real ) ] :Optional :Start Angle [Degree] of Ref for Rot2; Def.: 0
+ [-startRot3 startRot3 (0.0 ).as(Real ) ] :Optional :Start Angle [Degree] of Ref for Rot3; Def.: 0
+ [-StackOrder StackOrder (0 ).as(Integer ) ] :Optional :Stack Order for Stacked 2D of references, refer to attention
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :Output: Parameter [mrcImage-format]
+ [-O[utput] OutASC (stdout ).as(outFile ) ] :Optional :Output: Parameter [ASCII]
+ [-cor[relation] corFile (NULL ).as(outFile ) ] :Optional :Correation Map at Maximum (Linear) [mrcImage-format]
+ [-cor[relation]2 corFile2 (NULL ).as(outFile ) ] :Optional :Correation Map2 at Maximum (Set Mode Correlation)[mrcImage-format]
+ [-cor[relation]All corAllFile (NULL ).as(outFile ) ] :Optional :Correation Map with All Rotation [mrcImage-format]
+ [-fit[tedToRef] fitFile (NULL ).as(outFile ) ] :Optional :Output: rotatedImage at Maximum(Linear Correlation) [mrcImage]
+ [-fit[tedToRef]2 fitFile2 (NULL ).as(outFile ) ] :Optional :Output: rotatedImage at Maximum(Set Correlation mode) [mrcImage]
+ [-RefineMode RefineMode (0 ).as(Integer ) ] :Optional :RefinementStep: Linear:0 or SetMode:1
+ [-n[umber] Rot (36 ).as(Real ) ] :Optional :Input: Rotation around the vertical axis against image plane: dRot = 360/n [degree]
+ [-range minAngle (-5.0 ).as(Real )
+ maxAngle (5.0 ).as(Real ) ] :Optional :Input: SearchRange: Rotation around the vertical axis against image plane
+ [-refStep1 refStep1 (1 ).as(Integer ) ] :Optional :SearchStep for Ref: Each Image along Rot1
+ [-refStep2 refStep2 (1 ).as(Integer ) ] :Optional :SearchStep for Ref: Each Image along Rot2
+ [-refStep3 refStep3 (1 ).as(Integer ) ] :Optional :SearchStep for Ref: Each Image along Rot3
+ [-nRot1Area nRot1AreaMin (-360 ).as(Real )
+ nRot1AreaMax (360 ).as(Real )
+ nRot1AreaStep (25 ).as(Real ) ] :Optional :number of Ref for Rot1
+ [-nRot2Area nRot2AreaMin (-360 ).as(Real )
+ nRot2AreaMax (360 ).as(Real )
+ nRot2AreaStep (25 ).as(Real ) ] :Optional :number of Ref for Rot2
+ [-nRot3Area nRot3AreaMin (-360 ).as(Real )
+ nRot3AreaMax (360 ).as(Real )
+ nRot3AreaStep (25 ).as(Real ) ] :Optional :number of Ref for Rot3
+ [-MagRange MagRangeMin (1.0 ).as(Real )
+ MagRangeMax (1.0 ).as(Real )
+ MagRangeStep (0.1 ).as(Real ) ] :Optional :Magnification Range
+ [-Iter[ation] Iter (1 ).as(Integer ) ] :Optional :Iteration for Rotation around the vertical axis against image plane
+ [-Method Method (0 ).as(Integer ) ] :Optional :0: Correlation, 1: SSDA
+ [-s[earchRegion] sminx (0 ).as(Real )
+ sminy (0 ).as(Real )
+ smaxx (0/*N.x-1*/).as(Real )
+ smaxy (0/*N.y-1*/).as(Real ) ] :Optional :SearchRegion [pixel]: used in lmrcImageAutoRotationCorrelation
+ [-Shift ] :Optional :Image Shift, when in > ref
+ [-RepeatX RepeatX (27.3 ).as(Real ) ] :Optional :RepeatX[A]
+ [-RepeatXDelta RepeatXDelta (5 ).as(Real ) ] :Optional :RepeatXDelta[A]
+ [-RepeatY RepeatY (27.3 ).as(Real ) ] :Optional :RepeatY[A]
+ [-RepeatYDelta RepeatYDelta (5 ).as(Real ) ] :Optional :RepeatYDelta[A]
+ [-Xshift ] :Optional :X-Shift Only
+ [-NoShift ] :Optional :No-Shift
+ [-Log Log (stdout ).as(outFile ) ] :Optional :Output: LogFile
+ [-pvm pvm (1 ).as(Integer ) ] :Optional :Task Number
+ [-pvmList pvmList (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Mode -----
When, -Method 0(Default:Correlation)
0: Normal Correlation FxG*
<PRE>
Usage: mrcImageAutoRotationCorrelation3D
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrc[test]
- [-r[ef] Ref (NULL )] :Essential :Input: mrc[ref]
- [-o[utput] Out (stdout )] :Optional :Output: Parameter
- [-cor Cor (NULL )] :Optional :Output: CorMap
- [-fit Fit (stdout )] :Optional :Output: Best Fit
- [-E[uler]A[ngle] EulerAngle (YOYS )] :Optional :Input: EulerAngle
- [-Rot1 Rot1Min (0.0 )Rot1Max (360.0 )Rot1Delta (5.0 )] :Optional :Rot1
- [-Rot2 Rot2Min (0.0 )Rot2Max (180.0 )Rot2Delta (5.0 )] :Optional :Rot2
- [-Rot3 Rot3Min (0.0 )Rot3Max (360.0 )Rot3Delta (5.0 )] :Optional :Rot3
- [-Xrange XrangeMin (0 )XrangeMax (0 )] :Optional :Xrange[pixel]: Not set, all space search
- [-Yrange YrangeMin (0 )YrangeMax (0 )] :Optional :Yrange[pixel]: Not set, all space search
- [-Zrange ZrangeMin (0 )ZrangeMax (0 )] :Optional :Zrange[pixel]: Not set, all space search
- [-M[ode] Mode (0 )] :Optional :Mode: Correlation Mode
- [-M[ode]R[otation] ModeRotation (0 )] :Optional :Mode: Rotation3D Mode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode: InterpolationMode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrc[test]
+ [-r[ef] Ref (NULL ).as(inFile ) ] :Essential :Input: mrc[ref]
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: Parameter
+ [-cor Cor (NULL ).as(outFile ) ] :Optional :Output: CorMap
+ [-fit Fit (stdout ).as(outFile ) ] :Optional :Output: Best Fit
+ [-E[uler]A[ngle] EulerAngle (YOYS ).as(String ) ] :Optional :Input: EulerAngle
+ [-Rot1 Rot1Min (0.0 ).as(Real )
+ Rot1Max (360.0 ).as(Real )
+ Rot1Delta (5.0 ).as(Real ) ] :Optional :Rot1
+ [-Rot2 Rot2Min (0.0 ).as(Real )
+ Rot2Max (180.0 ).as(Real )
+ Rot2Delta (5.0 ).as(Real ) ] :Optional :Rot2
+ [-Rot3 Rot3Min (0.0 ).as(Real )
+ Rot3Max (360.0 ).as(Real )
+ Rot3Delta (5.0 ).as(Real ) ] :Optional :Rot3
+ [-Xrange XrangeMin (0 ).as(Real )
+ XrangeMax (0 ).as(Real ) ] :Optional :Xrange[pixel]: Not set, all space search
+ [-Yrange YrangeMin (0 ).as(Real )
+ YrangeMax (0 ).as(Real ) ] :Optional :Yrange[pixel]: Not set, all space search
+ [-Zrange ZrangeMin (0 ).as(Real )
+ ZrangeMax (0 ).as(Real ) ] :Optional :Zrange[pixel]: Not set, all space search
+ [-M[ode] Mode (0 ).as(Integer ) ] :Optional :Mode: Correlation Mode
+ [-M[ode]R[otation] ModeRotation (0 ).as(Integer ) ] :Optional :Mode: Rotation3D Mode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode: InterpolationMode
----- Additional Usage -----
----- -M CorrelationMode -----
0: Normal Correlation FxG*
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImageAutoTriming</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAutoTriming</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageAutoTriming
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:mrcImage
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output:mrcImage
+ [-O[utput] OutParam (stdout ).as(outFile::YAML ) ] :Optional :OutputParams:YAML
+ [-E[uler]A[ngle]Mode EAMode (ZONS ).as(String ) ] :Optional :EulerAngle
+ [-Rot[ation]1 Rot1Min (-5 ).as(Real )
+ Rot1Max (5 ).as(Real )
+ Rot1Delta (1 ).as(Real ) ] :Optional :Rot1
+ [-Rot[ation]2 Rot2Min (-5 ).as(Real )
+ Rot2Max (5 ).as(Real )
+ Rot2Delta (1 ).as(Real ) ] :Optional :Rot2
+ [-Rot[ation]3 Rot3Min (-5 ).as(Real )
+ Rot3Max (5 ).as(Real )
+ Rot3Delta (1 ).as(Real ) ] :Optional :Rot3
+ [-M[ode] InterpolationMode (0 ).as(Integer ) ] :Optional :Iterpolation Mode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+>>> mode
+0: z-layer(minimum of z-axis by min)
+1: z-layer(minimum of z-axis by SD)
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: mrcImageAverage
Options:
- [-i[nput] In (NULL )] :Essential :Input: Image File List
- [-w[eight] InWeight (NULL )] :Optional :Input: Weight File List
- [-o[utput] Out (NULL )] :Essential :Output: Average
- [-o[utput]W[eight] OutWeight (NULL )] :Optional :Output: Weight
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFileList ) ] :Essential :Input: Image File List
+ [-w[eight] InWeight (NULL ).as(inFileList ) ] :Optional :Input: Weight File List
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: Average
+ [-o[utput]W[eight] OutWeight (NULL ).as(outFile ) ] :Optional :Output: Weight
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageBandPassFilter
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-h[alf]v[aluepoint]l[ow]hvl (1.0 )] :Optional :HalfValuePointLow
- [-h[alf]v[aluepoint]h[igh]hvh (1.0 )] :Optional :HalfValuePointHigh
- [-w[idth]l[ow] wl (1.0 )] :Optional :WidthOfDumpingLow
- [-w[idth]h[igh] wh (1.0 )] :Optional :WidthOfDumpingHigh
- [-lowweight lowWeight (0.0 )] :Optional :Weight of Low Freq.
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-h[alf]v[aluepoint]l[ow]hvl (1.0 ).as(Real ) ] :Optional :HalfValuePointLow
+ [-h[alf]v[aluepoint]h[igh]hvh (1.0 ).as(Real ) ] :Optional :HalfValuePointHigh
+ [-w[idth]l[ow] wl (1.0 ).as(Real ) ] :Optional :WidthOfDumpingLow
+ [-w[idth]h[igh] wh (1.0 ).as(Real ) ] :Optional :WidthOfDumpingHigh
+ [-lowweight lowWeight (0.0 ).as(Real ) ] :Optional :Weight of Low Freq.
>>> Mode <<<<
1: Step filter : required argumnent: -hvl -hvh
2: Cos filter : required argumnent: -hvl -hvh -wl -wh
<PRE>
Usage: mrcImageBilateralFilter
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-s[igma]D[ensity] SigmaDensity (2.0 )] :Optional :SigmaDensity
- [-k[ernal]T[type]D[ensity]KernelTypeDensity (0 )] :Optional :KernelTypeForDensity
- [-s[igma]S[pace] SigmaSpace (1.0 )] :Optional :SigmaSpace
- [-s[igma]S[pace]3 SigmaSpaceX (1.0 )SigmaSpaceY (1.0 )SigmaSpaceZ (1.0 )] :Optional :SigmaSpace(3D)
- [-k[ernel]T[ype]S[pace]KernelTypeSpace (0 )] :Optional :KernelTypeForSpace
- [-k[ernel]S[ize] KernelSize (5 )] :Optional :KernelSize
- [-k[ernel]S[ize]3 KernelSizeX (5 )KernelSizeY (5 )KernelSizeZ (5 )] :Optional :KernelSize(3D)
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-s[igma]D[ensity] SigmaDensity (2.0 ).as(Real ) ] :Optional :SigmaDensity
+ [-k[ernal]T[type]D[ensity]KernelTypeDensity (0 ).as(Integer ) ] :Optional :KernelTypeForDensity
+ [-s[igma]S[pace] SigmaSpace (1.0 ).as(Real ) ] :Optional :SigmaSpace
+ [-s[igma]S[pace]3 SigmaSpaceX (1.0 ).as(Real )
+ SigmaSpaceY (1.0 ).as(Real )
+ SigmaSpaceZ (1.0 ).as(Real ) ] :Optional :SigmaSpace(3D)
+ [-k[ernel]T[ype]S[pace]KernelTypeSpace (0 ).as(Integer ) ] :Optional :KernelTypeForSpace
+ [-k[ernel]S[ize] KernelSize (5 ).as(Integer ) ] :Optional :KernelSize
+ [-k[ernel]S[ize]3 KernelSizeX (5 ).as(Integer )
+ KernelSizeY (5 ).as(Integer )
+ KernelSizeZ (5 ).as(Real ) ] :Optional :KernelSize(3D)
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
Bilateral Filter
by Tomashi and Manduchi
<PRE>
Usage: mrcImageBinalization
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-t[hreshold] t (0 )] :Optional :Value of threshold
- [-v[alue] v (0 )] :Optional :Value
- [-near near (0 )] :Optional :Near[pixel]: Near-area also binary
- [-nLevel nLevel (256 )] :Optional :nLevel: For creating histgram by Kittler and Ohtsu
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-p[tile] p (0.5 )] :Optional :p
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:mrcImage
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output:mrcImage
+ [-O[utput] OutParam (stdout ).as(outFile::ASCII ) ] :Optional :Output:Parameters
+ [-t[hreshold] t (0 ).as(Real ) ] :Optional :Value of threshold
+ [-d[elta]t[hreshold] deltaThreshold (0 ).as(Real ) ] :Optional :Difference threshold
+ [-s[igma]t[hreshold] sigmaThreshold (0.5 ).as(Real ) ] :Optional :Sigma threshold(BandPath)
+ [-v[alue] v (0 ).as(Real ) ] :Optional :Value
+ [-near near (0 ).as(Real ) ] :Optional :Near[pixel]: Near-area also binary
+ [-nLevel nLevel (256 ).as(Integer ) ] :Optional :nLevel: For creating histgram by Kittler and Ohtsu
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-p[tile] p (0.5 ).as(Real ) ] :Optional :p
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- Additional Usage -----
mode 0: Under thresHold, 0. Above thresHold, 1.
1: Above thresHold, 0. Under thresHold, 1.
2: Under thresHold, value. Above thresHold, unchanged.
3: Above thresHold, value. Under thresHold, unchanged.
- 16: Automatically Determine threshold by Kittler Method
- 32: Automatically Determine threshold by Ohtsu Method
- 48: Automatically Determine threshold by p-tile Method
+ 4: thresHold +- sigma, 1. Others 0.
+ 5: thresHold +- sigma, 0. Others 1.
+ 6: thresHold +- sigma, unchanged. Others value.
+ 7: thresHold +- sigma, value. Others unchanged.
+ +16: Automatically Determine threshold by Kittler Method
+ +32: Automatically Determine threshold by Ohtsu Method
+ +48: Automatically Determine threshold by p-tile Method
p range: 0.0 - 1.0
- 64: Automatically Determine threshold by Differential-Histogram Method
- 80: Automatically Determine threshold by Laplacian-Histogram Method
+ +64: Automatically Determine threshold by Differential-Histogram Method
+ +80: Automatically Determine threshold by Laplacian-Histogram Method
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageBlockMerge
Options:
- [-I[nput array of file]In (stdin )] :Essential :InputDataFiles
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-I[nput array of file]In (stdin ).as(inFileListNoOpen ) ] :Essential :InputDataFiles
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageBoundaryInfo
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrc-format
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: ascii
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageCCDNoiseRemove
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrc
- [-N[oise] InNoise (NULL )] :Essential :Input: noise information
- [-o[utput] Out (NULL )] :Essential :Output: mrc
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrc
+ [-N[oise] InNoise (NULL ).as(inFile ) ] :Essential :Input: noise information
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: mrc
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
mode: 0 random values
mode: 1 neighbor point's values
<PRE>
Usage: mrcImageCTFCompensation
Options:
- [-i[nput] In (stdin )] :Essential :InputFile
- [-o[utput] Out (stdout )] :Essential :OutputDataFile
- [-info[mation] Info (NULL )] :Optional :InformationFile(Essense only)
- [-info[mation]2 Info2 (NULL )] :Optional :InformationFile2(Display2 ctfinfo format)
- [-kV kV (200 )] :Optional :AccVol[kV]
- [-Cs Cs (2.1 )] :Optional :Cs[mm]
- [-df Defocus (27000 )] :Optional :Defocus[A]:under(+)
- [-white WhiteNoise (0.1 )] :Optional :WhiteNoise(N/S)
- [-SinWin SinWinRmin (0.1 )SinWinRmax (1.0 )] :Optional :Windowing by sine function from Rmin[/A] to Rmax[/A].Default: No Window.
- [-A[mplitude contrast]Amp (0.1 )] :Optional :The ratio of amplitude contrast to phase contrast
- [-Astig[matism] dfMin (0 )dfMax (0 )asAxis (0 )] :Optional :With Astigmatism
- [-NoAstig[matism] ] :Optional :Without Astigmatism
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (stdin ).as(inFile ) ] :Essential :InputFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Essential :OutputDataFile
+ [-info[mation] Info (NULL ).as(inFile ) ] :Optional :InformationFile(Essense only)
+ [-info[mation]2 Info2 (NULL ).as(inFile ) ] :Optional :InformationFile2(Display2 ctfinfo format)
+ [-kV kV (200 ).as(Real ) ] :Optional :AccVol[kV]
+ [-Cs Cs (2.1 ).as(Real ) ] :Optional :Cs[mm]
+ [-df Defocus (27000 ).as(Real ) ] :Optional :Defocus[A]:under(+)
+ [-white WhiteNoise (0.1 ).as(Real ) ] :Optional :WhiteNoise(N/S)
+ [-SinWin SinWinRmin (0.1 ).as(Real )
+ SinWinRmax (1.0 ).as(Real ) ] :Optional :Windowing by sine function from Rmin[/A] to Rmax[/A].Default: No Window.
+ [-A[mplitude contrast]Amp (0.1 ).as(Real ) ] :Optional :The ratio of amplitude contrast to phase contrast
+ [-Astig[matism] dfMin (0 ).as(Real )
+ dfMax (0 ).as(Real )
+ asAxis (0 ).as(Real ) ] :Optional :With Astigmatism
+ [-NoAstig[matism] ] :Optional :Without Astigmatism
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- mode -----
mode 0: No Correction
mode 1: x ctf/|ctf|, phase flipping
<PRE>
Usage: mrcImageCTFCompensationForTiltImage
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-I[nformation] Info (NULL )] :Essential :Infomation
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [cut[Back] cut (6 )] :Optional :Cut
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-I[nformation] Info (NULL ).as(inFile ) ] :Essential :Infomation
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [cut[Back] cut (6 ).as(Integer ) ] :Optional :Cut
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageCTFDetermination
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-r[eference] Ref (NULL )] :Essential :ReferenceDataFile
- [-o[utput] Out (stdout )] :Optional :Output Optimum [text]
- [-oP[utput] Out2 (NULL )] :Optional :Output Distribution [mrc image]
- [-oC[utput] OutC (NULL )] :Optional :Output CTF Information file
- [-oF[utput] OutF (NULL )] :Optional :Output Result FFT[mrc image]
- [-kV kV (200 )] :Optional :AccVol[kV]
- [-Cs Cs (2.1 )] :Optional :Cs[mm]
- [-Ain Ain (0.02 )] :Optional :IlluminationAperture[mrad]
- [-W[hiteNoise] WhiteNoise (1.0 )] :Optional :
- [-df mindf (0.0 )maxdf (200000 )deldf (1000 )] :Optional :df[A] for in
- [-AoverP minAoverP (0.0 )maxAoverP (1.0 )delAoverP (0.01 )] :Optional :AoverP[A] for in
- [-Rmin Rmin (0.0 )] :Optional :Rmin[/A]
- [-Rmax Rmax (0.1 )] :Optional :Rmax[/A]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode]F[ilter type]mF (1 )] :Optional :Filter Type
- [-m[ode]W[ight type] mW (0 )] :Optional :Wight Type
- [-m[ode]S[um type] mS (0 )] :Optional :Sum Type
- [-m[ode]C[TF Info type]mC (0 )] :Optional :CTF Information Type
- [-M[ode] M (0 )] :Optional :ref Type
- [-PixelSize PixelSize (5 )] :Optional :Pixel Size [A]
- [-Width Width (120 )] :Optional :Pad Width [pixel]
- [-truePitch truePitch (430 )] :Optional :True Pitch [A]
- [-dfRef firstDf (70000 )withinDf (1000 )] :Optional :dfRef for ref
- [-AoverPRef firstAoverP (0.05 )withinAoverP (0.01 )] :Optional :A over P Ref for ref
- [-MaxIter maxiter (10 )] :Optional :MaxIteration for ref
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-r[eference] Ref (NULL ).as(inFile ) ] :Essential :ReferenceDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output Optimum [text]
+ [-oP[utput] Out2 (NULL ).as(outFile ) ] :Optional :Output Distribution [mrc image]
+ [-oC[utput] OutC (NULL ).as(outFile ) ] :Optional :Output CTF Information file
+ [-oF[utput] OutF (NULL ).as(outFile ) ] :Optional :Output Result FFT[mrc image]
+ [-kV kV (200 ).as(Real ) ] :Optional :AccVol[kV]
+ [-Cs Cs (2.1 ).as(Real ) ] :Optional :Cs[mm]
+ [-Ain Ain (0.02 ).as(Real ) ] :Optional :IlluminationAperture[mrad]
+ [-W[hiteNoise] WhiteNoise (1.0 ).as(Real ) ] :Optional :
+ [-df mindf (0.0 ).as(Real )
+ maxdf (200000 ).as(Real )
+ deldf (1000 ).as(Real ) ] :Optional :df[A] for in
+ [-AoverP minAoverP (0.0 ).as(Real )
+ maxAoverP (1.0 ).as(Real )
+ delAoverP (0.01 ).as(Real ) ] :Optional :AoverP[A] for in
+ [-Rmin Rmin (0.0 ).as(Real ) ] :Optional :Rmin[/A]
+ [-Rmax Rmax (0.1 ).as(Real ) ] :Optional :Rmax[/A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode]F[ilter type]mF (1 ).as(Integer ) ] :Optional :Filter Type
+ [-m[ode]W[ight type] mW (0 ).as(Integer ) ] :Optional :Wight Type
+ [-m[ode]S[um type] mS (0 ).as(Integer ) ] :Optional :Sum Type
+ [-m[ode]C[TF Info type]mC (0 ).as(Integer ) ] :Optional :CTF Information Type
+ [-M[ode] M (0 ).as(Integer ) ] :Optional :ref Type
+ [-PixelSize PixelSize (5 ).as(Integer ) ] :Optional :Pixel Size [A]
+ [-Width Width (120 ).as(Integer ) ] :Optional :Pad Width [pixel]
+ [-truePitch truePitch (430 ).as(Real ) ] :Optional :True Pitch [A]
+ [-dfRef firstDf (70000 ).as(Real )
+ withinDf (1000 ).as(Real ) ] :Optional :dfRef for ref
+ [-AoverPRef firstAoverP (0.05 ).as(Real )
+ withinAoverP (0.01 ).as(Real ) ] :Optional :A over P Ref for ref
+ [-MaxIter maxiter (10 ).as(Integer ) ] :Optional :MaxIteration for ref
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- mrcFile -----
in <- Original Image
<PRE>
Usage: mrcImageCTFObservation
Options:
- [-i[nput] In (stdin )] :Essential :InputFile
- [-o[utput] Out (stdout )] :Essential :OutputDataFile
- [-kV kV (200 )] :Optional :AccVol[kV]
- [-Cs Cs (2.1 )] :Optional :Cs[mm]
- [-df Defocus (27000 )] :Optional :Defocus [A]:under(+)
- [-A AoverP (0.0 )] :Optional :AmplitudeContrast/PhaseContrast
- [-Ain Ain (0.0 )] :Optional :IlluminationAperture[mrad]
- [-white WhiteNoise (1.0 )] :Optional :WhiteNoise(N/S)
- [-SinWin SinWinRmin (0.1 )SinWinRmax (1.0 )] :Optional :Windowing by sine function from Rmin[A] to Rmax[A]
- [-ctfMode ctfMode (0 )] :Optional :CTFMode
- [-Astig[matism] dfMin (0 )dfMax (0 )asAxis (0 )] :Optional :With Atigmatism
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (stdin ).as(inFile ) ] :Essential :InputFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Essential :OutputDataFile
+ [-kV kV (200 ).as(Real ) ] :Optional :AccVol[kV]
+ [-Cs Cs (2.1 ).as(Real ) ] :Optional :Cs[mm]
+ [-df Defocus (27000 ).as(Real ) ] :Optional :Defocus [A]:under(+)
+ [-A AoverP (0.0 ).as(Real ) ] :Optional :AmplitudeContrast/PhaseContrast
+ [-Ain Ain (0.0 ).as(Real ) ] :Optional :IlluminationAperture[mrad]
+ [-white WhiteNoise (1.0 ).as(Real ) ] :Optional :WhiteNoise(N/S)
+ [-SinWin SinWinRmin (0.1 ).as(Real )
+ SinWinRmax (1.0 ).as(Real ) ] :Optional :Windowing by sine function from Rmin[A] to Rmax[A]
+ [-ctfMode ctfMode (0 ).as(Integer ) ] :Optional :CTFMode
+ [-Astig[matism] dfMin (0 ).as(Real )
+ dfMax (0 ).as(Real )
+ asAxis (0 ).as(Real ) ] :Optional :With Atigmatism
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- ctfMode -----
-ctfMode 0 : Phase Only
-ctfMode 1 : Phase and Amplitude
<PRE>
Usage: mrcImageCTFSN
Options:
- [-i[nput] In (stdin )] :Essential :InputFile
- [-o[utput] Out (stdout )] :Essential :OutputDataFile
- [-kV kV (200 )] :Optional :AccVol[kV]
- [-Cs Cs (1.7 )] :Optional :Cs[mm]
- [-df Defocus (2.7 )] :Essential :Defocus[A]:under(+)
- [-n1 deg1 (2 )] :Optional :Degree of zero point minimum
- [-n2 deg2 (4 )] :Optional :Degree of zero point maximum
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (stdin ).as(inFile ) ] :Essential :InputFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Essential :OutputDataFile
+ [-kV kV (200 ).as(Real ) ] :Optional :AccVol[kV]
+ [-Cs Cs (1.7 ).as(Real ) ] :Optional :Cs[mm]
+ [-df Defocus (2.7 ).as(Real ) ] :Essential :Defocus[A]:under(+)
+ [-n1 deg1 (2 ).as(Integer ) ] :Optional :Degree of zero point minimum
+ [-n2 deg2 (4 ).as(Integer ) ] :Optional :Degree of zero point maximum
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageCVE
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-sx sx (25 )] :Optional :x of Kernel Size
- [-sy sy (25 )] :Optional :y of Kernel Size
- [-sz sz (1 )] :Optional :z of Kernel Size
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-sx sx (25 ).as(Integer ) ] :Optional :x of Kernel Size
+ [-sy sy (25 ).as(Integer ) ] :Optional :y of Kernel Size
+ [-sz sz (1 ).as(Integer ) ] :Optional :z of Kernel Size
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageCenterDensityChange
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-r[adius]min rmin (0 )] :Optional :min radius[A]
- [-r[adius]max rmax (90 )] :Optional :max radius[A]
- [-ratio ratio (0 )] :Optional :ratio
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-M[ode] radiusMode (0 )] :Optional :radiusMode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-r[adius]min rmin (0 ).as(Real ) ] :Optional :min radius[A]
+ [-r[adius]max rmax (90 ).as(Real ) ] :Optional :max radius[A]
+ [-ratio ratio (0 ).as(Real ) ] :Optional :ratio
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-M[ode] radiusMode (0 ).as(Integer ) ] :Optional :radiusMode
----- Additional Usage -----
----- radiusMode -----
0:
<PRE>
Usage: mrcImageCenterGet
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-Nx[Number of x] Nx (0 )] :Optional :Nx:Default Nx of inputfile
- [-Ny[Number of y] Ny (0 )] :Optional :Ny:Default Ny of inputfile
- [-Nz[Number of z] Nz (0 )] :Optional :Nz:Default Nz of inputfile
- [-Cx[Center x] Cx (0 )] :Optional :Cetnter x position of extracted image.Default is center of iuput image.
- [-Cy[Center y] Cy (0 )] :Optional :Cetnter y position of extracted image.Default is center of iuput image.
- [-Cz[Center z] Cz (0 )] :Optional :Cetnter z position of extracted image.Default is center of iuput image.
- [-even ] :Optional :all dimensions of N are even.
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-M[ode2] mode2 (0 )] :Optional :Mode2
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-Nx[Number of x] Nx (0 ).as(Integer ) ] :Optional :Nx:Default Nx of inputfile
+ [-Ny[Number of y] Ny (0 ).as(Integer ) ] :Optional :Ny:Default Ny of inputfile
+ [-Nz[Number of z] Nz (0 ).as(Integer ) ] :Optional :Nz:Default Nz of inputfile
+ [-Cx[Center x] Cx (0 ).as(Real ) ] :Optional :Cetnter x position of extracted image.Default is center of iuput image.
+ [-Cy[Center y] Cy (0 ).as(Real ) ] :Optional :Cetnter y position of extracted image.Default is center of iuput image.
+ [-Cz[Center z] Cz (0 ).as(Real ) ] :Optional :Cetnter z position of extracted image.Default is center of iuput image.
+ [-even ] :Optional :all dimensions of N are even.
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-M[ode2] mode2 (0 ).as(Integer ) ] :Optional :Mode2
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageCenterOfMassCalculate
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (stdout )] :Optional :InputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :InputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImageChainCodeCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageChainCodeCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageChainCodeCalc
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+>> mode
+ 0: 8-neighbor, chainCode absolute
+ 1: 4-neighbor, chainCode absolute
+ 2: 8-neighbor, chainCode relative
+ 3: 4-neighbor, chainCode relative
+ </PRE>
+</BODY>
+</HTML>
<PRE>
Usage: mrcImageCircumferentialProjection
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-dang dang (10 )] :Optional :Delta Angle[degree]
- [-zmin zmin (0 )] :Optional :Z Minimum[A]
- [-zmax zmax (100 )] :Optional :Z Maximum[A]
- [-dz dz (10 )] :Optional :Delta Z[A]
- [-rmin rmin (0 )] :Optional :Radius Minimum[A]
- [-rmax rmax (200 )] :Optional :Radius Maximum[A]
- [-threshold threshold (0 )] :Optional :Set threshold value. Averaged density is more than threshold value
- [-dr dr (10 )] :Optional :Delta Radius[A]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-dang dang (10 ).as(Real ) ] :Optional :Delta Angle[degree]
+ [-zmin zmin (0 ).as(Real ) ] :Optional :Z Minimum[A]
+ [-zmax zmax (100 ).as(Real ) ] :Optional :Z Maximum[A]
+ [-dz dz (10 ).as(Real ) ] :Optional :Delta Z[A]
+ [-rmin rmin (0 ).as(Real ) ] :Optional :Radius Minimum[A]
+ [-rmax rmax (200 ).as(Real ) ] :Optional :Radius Maximum[A]
+ [-threshold threshold (0 ).as(Real ) ] :Optional :Set threshold value. Averaged density is more than threshold value
+ [-dr dr (10 ).as(Real ) ] :Optional :Delta Radius[A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
x --> r
y --> z
<PRE>
Usage: mrcImageClosing
Options:
- [-i[nput] In (NULL )] :Essential :Input: MRC
- [-o[utput] Out (NULL )] :Essential :Output: MRC
- [-times times (1 )] :Optional :Times: erosion*times -> dilation*times
- [-o[utput]SE OutSE (NULL )] :Optional :Output: MRC(SE)
- [-S[tructuring]E[lement]SEmode (0 )] :Optional :StructuringElement
- [-r[adius] radius (2 )] :Optional :Radius
- [-n n (5 )] :Optional :size
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: MRC
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: MRC
+ [-times times (1 ).as(Integer ) ] :Optional :Times: erosion*times -> dilation*times
+ [-o[utput]SE OutSE (NULL ).as(outFile ) ] :Optional :Output: MRC(SE)
+ [-S[tructuring]E[lement]SEmode (0 ).as(Integer ) ] :Optional :StructuringElement
+ [-r[adius] radius (2 ).as(Integer ) ] :Optional :Radius
+ [-n n (5 ).as(Integer ) ] :Optional :size
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- Structuring Element : Mode
0: 2D Cross3x3: 4-neighbour
1: 2D Square3x3: 8-neighbour
-2: 2D Open Disk , need (radius, n)
+2: 2D Disk , need (radius, n(squre size))
3: 3D Cross3x3x3: 6-neighbour
4: 3D Cubic3x3x3: 26-neighbour
-5: 3D Open Disk , need (radius, n)
+5: 3D Sphere, need (radius, n(cubic size))
+6: 2D Rectangle, need nx, ny
+7: 3D Cuboid, need nx, ny, nz
+8: 3D Cylindar, need r, nx, ny, nz
-----
Dilation: Max for image : Or for binary image
Erosion: Min for image : And for binary image
<PRE>
Usage: mrcImageClusterAnalysis
Options:
- [-I[nput array of file]In (NULL )] :Essential :InputDataFiles
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-O[utput] ] :Optional :Output: averaged images: filename is xxxx.avg: xxxx is input filename.
- [-N[umberOfClusters] N (1 )] :Optional :Number of clusters
- [-Min[imumCorrelation]Min (0.0 )] :Optional :Minimum: Correlation: Conditions for ending
- [-Iter[ation] ] :Optional :IterationFlag
- [-A[uto]R[otation] AutoRotation (72 )] :Optional :AutoRotation: rotation divided by this value
- [-A[utoRot]Range ARMin (0 )ARMax (360 )] :Optional :AutoRotationRange
- [-A[uto]R[otation]iter[ation]AutoRotationIteration(2 )] :Optional :AutoRotationIteration
- [-A[uto]R[otation]MethodAutoRotationMethod (0 )] :Optional :Method for Correlation for Auto Rotation
- [-M[odeForCorrelation]correlationMode (19 )] :Optional :Correlation Mode for AutoRotation
- [-pvm ] :Optional :Parallel Analysis by PVM
- [-pvmList pvmList (NULL )] :Optional :pvmList: Input
- [-Log Log (stdout )] :Optional :Log: Output
- [-Log2 Log2 (NULL )] :Optional :Log2: Output: ClusterNode Only
- [-LogIn LogIn (NULL )] :Optional :previousLog: Input
- [-prevF[ileNum] prevFileNum (0 )] :Optional :previousLogFileNum: Input
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (2 )] :Optional :Mode
+ [-I[nput array of file]In (NULL ).as(inFileListNoOpen ) ] :Essential :InputDataFiles
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-O[utput] ] :Optional :Output: averaged images: filename is xxxx.avg: xxxx is input filename.
+ [-N[umberOfClusters] N (1 ).as(Integer ) ] :Optional :Number of clusters
+ [-Min[imumCorrelation]Min (0.0 ).as(Real ) ] :Optional :Minimum: Correlation: Conditions for ending
+ [-Iter[ation] ] :Optional :IterationFlag
+ [-A[uto]R[otation] AutoRotation (72 ).as(Integer ) ] :Optional :AutoRotation: rotation divided by this value
+ [-A[utoRot]Range ARMin (0 ).as(Real )
+ ARMax (360 ).as(Real ) ] :Optional :AutoRotationRange
+ [-A[uto]R[otation]iter[ation]AutoRotationIteration(2 ).as(Integer ) ] :Optional :AutoRotationIteration
+ [-A[uto]R[otation]MethodAutoRotationMethod (0 ).as(Integer ) ] :Optional :Method for Correlation for Auto Rotation
+ [-M[odeForCorrelation]correlationMode (19 ).as(Integer ) ] :Optional :Correlation Mode for AutoRotation
+ [-Log Log (stdout ).as(appendFile ) ] :Optional :Log: Output
+ [-Log2 Log2 (NULL ).as(appendFile ) ] :Optional :Log2: Output: ClusterNode Only
+ [-LogIn LogIn (NULL ).as(inFile ) ] :Optional :previousLog: Input
+ [-prevF[ileNum] prevFileNum (0 ).as(Integer ) ] :Optional :previousLogFileNum: Input
+ [-pthread pthread (0 ).as(Integer ) ] :Optional :pthread: Input
+ [-NoRecalc ] :Optional :No recalculation of distances
+ [-pvm ] :Optional :Parallel Analysis by PVM
+ [-pvmList pvmList (NULL ).as(inFile ) ] :Optional :pvmList: Input
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (2 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
Distance between clusters: mode
mode 0: By Correlation
-<HTML>
-<HEAD>
-<TITLE>mrcImageColoring</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageColoring</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageColoring
-Options:
- [-r[ed] rIn (NULL )] :Optional :Red:InputDataFile
- [-g[reen] gIn (NULL )] :Optional :Green:InputDataFile
- [-b[lue] bIn (NULL )] :Optional :Blue:InputDataFile
- [-rH[ight] rHigh (1 )] :Optional :Red:HighThres
- [-rL[ow] rLow (0 )] :Optional :Red:LowThres
- [-gH[ight] gHigh (1 )] :Optional :Green:HighThres
- [-gL[ow] gLow (0 )] :Optional :Green:LowThres
- [-bH[ibht] bHigh (1 )] :Optional :Blue:HibhThres
- [-bL[ow] bLow (0 )] :Optional :BLue:LowThres
- [-o[utput] Out (NULL )] :Optional :gif:OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageColoring: No such file or directory
<PRE>
Usage: mrcImageCommonLineSearch
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrc
- [-r[ef] Ref (NULL )] :Essential :Input: ref
- [-dtheta dtheta (1.0 )] :Optional :Input: degree
- [-o[utput] Out (stdout )] :Optional :Output: OptimalParameter
- [-O[utput] Out2 (NULL )] :Optional :Output: ParameterImage
- [-M[ode] searchMode (1 )] :Optional :SearchMode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrc
+ [-r[ef] Ref (NULL ).as(inFile ) ] :Essential :Input: ref
+ [-dtheta dtheta (1.0 ).as(Real ) ] :Optional :Input: degree
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: OptimalParameter
+ [-O[utput] Out2 (NULL ).as(outFile ) ] :Optional :Output: ParameterImage
+ [-M[ode] searchMode (1 ).as(Integer ) ] :Optional :SearchMode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
>>>> lmrcImageCommonLineInfo
---- mode ----
<PRE>
Usage: mrcImageConnection
Options:
- [-i[nput]1 In1 (NULL )] :Essential :InputDataFile
- [-i[nput]2 In2 (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput]1 In1 (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i[nput]2 In2 (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
-m 0: z connection
</PRE>
<PRE>
Usage: mrcImageConnectivityNumberCalc
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-f[orm] form (0 )] :Optional :Form
- [-I[nvers] invers (0 )] :Optional :Invers
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-f[orm] form (0 ).as(Integer ) ] :Optional :Form
+ [-I[nvers] invers (0 ).as(Integer ) ] :Optional :Invers
----- Additional Usage -----
mode 0 : Four Neighborhood. [default] : For 2 Dimension.
1 : Eight Nieghborhood. :
<PRE>
Usage: mrcImageContourSurfaceCreate
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrc
- [-o[utput] Out (NULL )] :Essential :Output: mrc
- [-C[ontour] Contour (0.0 )] :Essential :Input: Contour Value
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrc
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: mrc
+ [-C[ontour] Contour (0.0 ).as(Real ) ] :Essential :Input: Contour Value
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
-m 0 : SimpleMethod
When a point has contour surfaces between six voxels (Upper-Downward Right-Left For-Back) and the point,
<PRE>
Usage: mrcImageConvolution
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrcImage
- [-i[nput]k[ernal]a[rray]InKernelArray (NULL )] :Optional :Input: Array
- [-i[nput]k[ernal]m[rc]InKernelMRC (NULL )] :Optional :Input: mrcImage
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-times times (1 )] :Optional :Repeat time
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrcImage
+ [-i[nput]k[ernal]a[rray]InKernelArray (NULL ).as(inFile ) ] :Optional :Input: Array
+ [-i[nput]k[ernal]m[rc]InKernelMRC (NULL ).as(inFile ) ] :Optional :Input: mrcImage
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-times times (1 ).as(Integer ) ] :Optional :Repeat time
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
>>> Array Format under Eos <<<<
ndim N0 N1 N2 ...
<PRE>
Usage: mrcImageCoordinateChange
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageCoreImageCalc
Options:
- [-i[nput] In (NULL )] :Essential :Input: Pretreated Core-loss Image
- [-e[neryg]l[oss] EL (180 )] :Essential :Input: EnergyLoss
- [-bg[List] BG (NULL )] :Essential :Input: Bg File List
- [-o[utput] Out (NULL )] :Essential :Output: Core-Loss Image
- [-O[utputBG] OutBG (NULL )] :Optional :Output: BG-Image
- [-Chi[sq] OutChi (NULL )] :Optional :Output: Chi-Image
- [-initial[Value] A1 (5040 )A2 (500 )A3 (-12 )] :Optional :Input: A1 + A2*EELS^A3
- [-limitA3 LimitA3Min (-16 )LimitA3Max (-5 )] :Optional :Input: limit A3
- [-baseEELS BaseEELS (160.0 )] :Optional :Input: BaseEELS as 1.0
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: Pretreated Core-loss Image
+ [-e[neryg]l[oss] EL (180 ).as(Real ) ] :Essential :Input: EnergyLoss
+ [-bg[List] BG (NULL ).as(inFileList ) ] :Essential :Input: Bg File List
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: Core-Loss Image
+ [-O[utputBG] OutBG (NULL ).as(outFile ) ] :Optional :Output: BG-Image
+ [-Chi[sq] OutChi (NULL ).as(outFile ) ] :Optional :Output: Chi-Image
+ [-initial[Value] A1 (5040 ).as(Real )
+ A2 (500 ).as(Real )
+ A3 (-12 ).as(Real ) ] :Optional :Input: A1 + A2*EELS^A3
+ [-limitA3 LimitA3Min (-16 ).as(Real )
+ LimitA3Max (-5 ).as(Real ) ] :Optional :Input: limit A3
+ [-baseEELS BaseEELS (160.0 ).as(Real ) ] :Optional :Input: BaseEELS as 1.0
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
>>> BGFile List
FileName1 EEL
<PRE>
Usage: mrcImageCorrelation
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Optional :OutputDataFile: Correlation Map
- [-O[utput] Out2 (NULL )] :Optional :OutputDataFile: Correlation Map for Refinement
- [-r[eference] Ref (NULL )] :Essential :ReferenceDataFile
- [-cor[relation]Info OutCor (stdout )] :Optional :Output: Correlation Info
- [-a[verage] Avg (NULL )] :Optional :OutputDataFile: Averaged File
- [-s[hit] Shift (NULL )] :Optional :OutputDataFile: Shifted InputFile
- [-refine RefineStep (0.25 )RefineRange (3.0 )RefineMode (2 )] :Optional :Refinemnet: Step Range[pixelUnit]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-M[ode2] mode2 (0 )] :Optional :Mode2
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile: Correlation Map
+ [-O[utput] Out2 (NULL ).as(outFile ) ] :Optional :OutputDataFile: Correlation Map for Refinement
+ [-r[eference] Ref (NULL ).as(inFile ) ] :Essential :ReferenceDataFile
+ [-cor[relation]Info OutCor (stdout ).as(outFile ) ] :Optional :Output: Correlation Info
+ [-a[verage] Avg (NULL ).as(outFile ) ] :Optional :OutputDataFile: Averaged File
+ [-s[hit] Shift (NULL ).as(outFile ) ] :Optional :OutputDataFile: Shifted InputFile
+ [-refine RefineStep (0.25 ).as(Real )
+ RefineRange (3.0 ).as(Real )
+ RefineMode (2 ).as(Integer ) ] :Optional :Refinemnet: Step Range[pixelUnit]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-M[ode2] mode2 (0 ).as(Integer ) ] :Optional :Mode2
----- Mode: -m -----
0: Normal Correlation FxG*
1: Phase Correlation FxG*/ |FxG*|
<PRE>
Usage: mrcImageCorrelationInFourierSpace
Options:
- [-i1[input1] In1 (NULL )] :Optional :InputDataFile
- [-i2[input2] In2 (NULL )] :Optional :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i1[input1] In1 (NULL ).as(inFile ) ] :Optional :InputDataFile
+ [-i2[input2] In2 (NULL ).as(inFile ) ] :Optional :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
Mode 0: (FxG*)/(|FG|)
Mode 1: Phase residual
<PRE>
Usage: mrcImageCrystalCreate
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-nx nx (1 )] :Optional :Number:x-axis
- [-ny ny (1 )] :Optional :Number:y-axis
- [-nz nz (1 )] :Optional :Number:z-axis
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-nx nx (1 ).as(Integer ) ] :Optional :Number:x-axis
+ [-ny ny (1 ).as(Integer ) ] :Optional :Number:y-axis
+ [-nz nz (1 ).as(Integer ) ] :Optional :Number:z-axis
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageCylinderSection
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-angmin angmin (0 )] :Optional :Angle Minimum[degree]
- [-angmax angmax (360 )] :Optional :Angle Maximum[degree]
- [-dang dang (10 )] :Optional :Delta Angle[degree]
- [-zmin zmin (0 )] :Optional :Z Minimum[A]
- [-zmax zmax (100 )] :Optional :Z Maximum[A]
- [-dz dz (10 )] :Optional :Delta Z[A]
- [-rmin rmin (0 )] :Optional :Radius Minimum[A]
- [-rmax rmax (250 )] :Optional :Radius Maximum[A]
- [-dr dr (10 )] :Optional :Delta Radius[A]
- [-W[eight] ] :Optional :Data are weithed by r
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-angmin angmin (0 ).as(Real ) ] :Optional :Angle Minimum[degree]
+ [-angmax angmax (360 ).as(Real ) ] :Optional :Angle Maximum[degree]
+ [-dang dang (10 ).as(Real ) ] :Optional :Delta Angle[degree]
+ [-zmin zmin (0 ).as(Real ) ] :Optional :Z Minimum[A]
+ [-zmax zmax (100 ).as(Real ) ] :Optional :Z Maximum[A]
+ [-dz dz (10 ).as(Real ) ] :Optional :Delta Z[A]
+ [-rmin rmin (0 ).as(Real ) ] :Optional :Radius Minimum[A]
+ [-rmax rmax (250 ).as(Real ) ] :Optional :Radius Maximum[A]
+ [-dr dr (10 ).as(Real ) ] :Optional :Delta Radius[A]
+ [-W[eight] ] :Optional :Data are weithed by r
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
Format Change
x --> ang
<PRE>
Usage: mrcImageDeadPixelCorrection
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-dp[dead point] Dp (NULL )] :Essential :DeadPointPositionFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-dp[dead point] Dp (NULL ).as(inFile ) ] :Essential :DeadPointPositionFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageDensityChangeEstimation
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrcImage
- [-i[nput]2 In2 (NULL )] :Essential :Input: mrcImage2
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrcImage
+ [-i[nput]2 In2 (NULL ).as(inFile ) ] :Essential :Input: mrcImage2
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- Attention !!!-----
In Eos system, positive values are regarded as density.
<PRE>
Usage: mrcImageDensityInfo
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-C[ontour] Contour (10 )] :Optional :ContourLevel: 10 6.953245e-310ach
- [-log Log (NULL )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-C[ontour] Contour (10 ).as(Real ) ] :Optional :ContourLevel: 10 5.533535e-322ach
+ [-log Log (NULL ).as(appendFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Attention !!!-----
In Eos system, positive values are regarded as density.
If a pixel has a negative value, the value of the pixel is regarded as zero.lmrcImageDensityInfo Mode:
<PRE>
Usage: mrcImageDensityNormalization
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrc
- [-o[utput] Out (NULL )] :Essential :Output: mrc
- [-V[alue] Value (100 )] :Optional :Output: value
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrc
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: mrc
+ [-V[alue] Value (100 ).as(Real ) ] :Optional :Output: value
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
Isovolume: 0 : make the sum of pixel values the input value
</PRE>
<PRE>
Usage: mrcImageDensityNormalizationByImage
Options:
- [-i[nput] In (NULL )] :Essential :Test: Input
- [-r[ef] Ref (NULL )] :Essential :Reference: Input
- [-o[utput] Out (NULL )] :Essential :NormalizedImage: Output
- [-O[utput] OutParam (stdout )] :Optional :Parameters: Output
- [-D[ataForNormalizing]UsedData (stdout )] :Optional :DataList to be used
- [-Cylinder CCenterX (20 )CCenterY (20 )CMinR (10 )CMaxR (20 )] :Optional :Cylinder Region
- [-testBG[Region] tstBGMin (-3 )tstBGMax (3 )tstBGDelta (0.1 )] :Optional :SearchRegion
- [-M[ode] fitMode (0 )] :Optional :DensityFittngMethod: Mode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Test: Input
+ [-r[ef] Ref (NULL ).as(inFile ) ] :Essential :Reference: Input
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :NormalizedImage: Output
+ [-O[utput] OutParam (stdout ).as(outFile ) ] :Optional :Parameters: Output
+ [-D[ataForNormalizing]UsedData (stdout ).as(outFile ) ] :Optional :DataList to be used
+ [-Cylinder CCenterX (20 ).as(Real )
+ CCenterY (20 ).as(Real )
+ CMinR (10 ).as(Real )
+ CMaxR (20 ).as(Real ) ] :Optional :Cylinder Region
+ [-testBG[Region] tstBGMin (-3 ).as(Real )
+ tstBGMax (3 ).as(Real )
+ tstBGDelta (0.1 ).as(Real ) ] :Optional :SearchRegion
+ [-M[ode] fitMode (0 ).as(Integer ) ] :Optional :DensityFittngMethod: Mode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- Mode -----
1: Sigma!=1.0
<PRE>
Usage: mrcImageDilation
Options:
- [-i[nput] In (NULL )] :Essential :Input: MRC
- [-o[utput] Out (NULL )] :Essential :Output: MRC
- [-o[utput]SE OutSE (NULL )] :Optional :Output: MRC(SE)
- [-S[tructuring]E[lement]SEmode (0 )] :Optional :StructuringElement
- [-r[adius] radius (2 )] :Optional :Radius
- [-n n (5 )] :Optional :size
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: MRC
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: MRC
+ [-o[utput]SE OutSE (NULL ).as(outFile ) ] :Optional :Output: MRC(SE)
+ [-S[tructuring]E[lement]SEmode (0 ).as(Integer ) ] :Optional :StructuringElement
+ [-r[adius] radius (2 ).as(Integer ) ] :Optional :Radius
+ [-n n (5 ).as(Integer ) ] :Optional :size
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- Structuring Element : Mode
0: 2D Cross3x3: 4-neighbour
1: 2D Square3x3: 8-neighbour
-2: 2D Open Disk , need (radius, n)
+2: 2D Disk , need (radius, n(squre size))
3: 3D Cross3x3x3: 6-neighbour
4: 3D Cubic3x3x3: 26-neighbour
-5: 3D Open Disk , need (radius, n)
+5: 3D Sphere, need (radius, n(cubic size))
+6: 2D Rectangle, need nx, ny
+7: 3D Cuboid, need nx, ny, nz
+8: 3D Cylindar, need r, nx, ny, nz
-----
Dilation: Max for image : Or for binary image
Erosion: Min for image : And for binary image
<PRE>
Usage: mrcImageDisplayDensityAsTempFactor
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-p[dbfile] Pdb (NULL )] :Essential :InputPdbFile
- [-v[alue] Value (1 )] :Optional :value to multiply density
- [-H[ighThreshold] H (0.0 )] :Optional :High Threshold
- [-L[owThreshold] L (1.0 )] :Optional :Low Threshold
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-p[dbfile] Pdb (NULL ).as(inFile ) ] :Essential :InputPdbFile
+ [-v[alue] Value (1 ).as(Real ) ] :Optional :value to multiply density
+ [-H[ighThreshold] H (0.0 ).as(Real ) ] :Optional :High Threshold
+ [-L[owThreshold] L (1.0 ).as(Real ) ] :Optional :Low Threshold
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageDistanceConversion
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-f[orm] form (0 )] :Optional :Form
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-f[orm] form (0 ).as(Integer ) ] :Optional :Form
----- Additional Usage -----
mode 0 : 4 Neighborhood. [default]
1 : 8 Neighborhood.
<PRE>
Usage: mrcImageDivideInfoForTomography
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [cut[Back] cut (6 )] :Optional :Cut
- [-d[ivide] divide (4 )] :Optional :Divide
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [cut[Back] cut (6 ).as(Integer ) ] :Optional :Cut
+ [-d[ivide] divide (4 ).as(Integer ) ] :Optional :Divide
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageDivideIntoTwoImages
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput]1 Out1 (NULL )] :Essential :OutputDataFile
- [-o[utput]2 Out2 (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput]1 Out1 (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-o[utput]2 Out2 (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- mode -----
0:Vertical to the longest axis.
1:Vertical to x axis
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImageEdgeCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageEdgeCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageEdgeCalc
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-n[eighbor] Neighbor (8 ).as(Integer ) ] :Optional :Neighbor
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: mrcImageEdgeImageGet
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrcImage
- [-o[utput] Out (NULL )] :Optional :Output: mrcImage
- [-s[ize] Size (64 )] :Optional :Size: [pixel]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrcImage
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :Output: mrcImage
+ [-s[ize] Size (64 ).as(Integer ) ] :Optional :Size: [pixel]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
mode:
0: 4 Edge (x-y plane) from Image(0-3)
<PRE>
Usage: mrcImageErosion
Options:
- [-i[nput] In (NULL )] :Essential :Input: MRC
- [-o[utput] Out (NULL )] :Essential :Output: MRC
- [-o[utput]SE OutSE (NULL )] :Optional :Output: MRC(SE)
- [-S[tructuring]E[lement]SEmode (0 )] :Optional :StructuringElement
- [-r[adius] radius (2 )] :Optional :Radius
- [-n n (5 )] :Optional :size
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input: MRC
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output: MRC
+ [-o[utput]SE OutSE (NULL ).as(outFile::mrcImage ) ] :Optional :Output: MRC(SE)
+ [-S[tructuring]E[lement]SEmode (0 ).as(Integer ) ] :Optional :StructuringElement
+ [-r[adius] radius (2 ).as(Integer ) ] :Optional :Radius
+ [-n n (5 ).as(Integer ) ] :Optional :size
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- Structuring Element : Mode
0: 2D Cross3x3: 4-neighbour
1: 2D Square3x3: 8-neighbour
-2: 2D Open Disk , need (radius, n)
+2: 2D Disk , need (radius, n(squre size))
3: 3D Cross3x3x3: 6-neighbour
4: 3D Cubic3x3x3: 26-neighbour
-5: 3D Open Disk , need (radius, n)
+5: 3D Sphere, need (radius, n(cubic size))
+6: 2D Rectangle, need nx, ny
+7: 3D Cuboid, need nx, ny, nz
+8: 3D Cylindar, need r, nx, ny, nz
-----
Dilation: Max for image : Or for binary image
Erosion: Min for image : And for binary image
<PRE>
Usage: mrcImageEstimateTiltImage
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-tiltAngle TiltAngle (0 )] :Optional :Tilt Angle[degree]
- [-tiltAxis TiltAxis (0 )] :Optional :Tilt Axis[degree]
- [-Inverse ] :Optional :To Non-tilt
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode: InterpolationMode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-tiltAngle TiltAngle (0 ).as(Real ) ] :Optional :Tilt Angle[degree]
+ [-tiltAxis TiltAxis (0 ).as(Real ) ] :Optional :Tilt Axis[degree]
+ [-Inverse ] :Optional :To Non-tilt
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode: InterpolationMode
----- Additional Usage -----
-i in :2D or 3D
</PRE>
<PRE>
Usage: mrcImageExpression
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-T[hreshold] Thres (1e-16 )] :Optional :Threshold to calculate.For mode 1 and 3.
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-T[hreshold] Thres (1e-16 ).as(Real ) ] :Optional :Threshold to calculate.For mode 1 and 3.
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- mode -----
0:Absolute value
-/bin/bash: mrcImageFFT: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>mrcImageFFT</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFFT</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFFT
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-cuda cudaDeviceID (0 ).as(Integer ) ] :Optional :UseCUDA
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+x, y and z must be even pixels.
+Excepts for like that
+(x, y, z)=(100, 1, 1)
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: mrcImageFFTLayerLineExtraction
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-[input] I[nformation]InI (NULL )] :Optional :InputDataFile
- [-truePitch truePitch (430 )] :Optional :true Pitch [A]
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-[input] I[nformation]InI (NULL ).as(inFile ) ] :Optional :InputDataFile
+ [-truePitch truePitch (430 ).as(Real ) ] :Optional :true Pitch [A]
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
Input File Format
FileName x z dY
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImageFFTSetsExtract</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFFTSetsExtract</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFFTSetsExtract
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:mrcImage
+ [-o[utput] FTBBase (out ).as(String ) ] :Essential :Output:basename-mrcImage(FT)s
+ [-O[utput] FTABase (Out ).as(String ) ] :Essential :Output:basename-ascii
+ [-W[idth] width (256 ).as(Integer ) ] :Optional :Width[pixel]
+ [-H[eight] height (256 ).as(Integer ) ] :Optional :Height[pixel]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: mrcImageFOMCalc
Options:
- [-i[nput] In (NULL )] :Optional :TestData
- [-w[eight] Weight (1.0 )] :Optional :Weight
- [-I[nput] InList (NULL )] :Optional :TestData Set
- [-r[ef] Ref (NULL )] :Essential :Ref, Model Data
- [-o[utput] Out (stdout )] :Optional :Output:
- [-RR[ange] Rmin (0.0 )Rmax (0.1 )] :Optional :Ring Range
- [-dR[ange] dR (0.0 )] :Optional :Ring Width
- [-nS[ector] nSector (1 )] :Optional :Sector Number
- [-dA[lpha] dAlpha (5 )] :Optional :delta Alpha
- [-XMax XMax (0.0 )] :Optional :Xmax: If not set, one calc Xmax
- [-A[uto]S[cale] ] :Optional :Auto Scaling
- [-A[llArea]A[uto]S[cale]AASRMax (0.05 )] :Optional :All Area Auto Scaling
- [-RS[cale] ] :Optional :R Scaling
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Optional :TestData
+ [-w[eight] Weight (1.0 ).as(Real ) ] :Optional :Weight
+ [-I[nput] InList (NULL ).as(inFileList ) ] :Optional :TestData Set
+ [-r[ef] Ref (NULL ).as(inFile ) ] :Essential :Ref, Model Data
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output:
+ [-RR[ange] Rmin (0.0 ).as(Real )
+ Rmax (0.1 ).as(Real ) ] :Optional :Ring Range
+ [-dR[ange] dR (0.0 ).as(Real ) ] :Optional :Ring Width
+ [-nS[ector] nSector (1 ).as(Integer ) ] :Optional :Sector Number
+ [-dA[lpha] dAlpha (5 ).as(Real ) ] :Optional :delta Alpha
+ [-XMax XMax (0.0 ).as(Real ) ] :Optional :Xmax: If not set, one calc Xmax
+ [-A[uto]S[cale] ] :Optional :Auto Scaling
+ [-A[llArea]A[uto]S[cale]AASRMax (0.05 ).as(Real ) ] :Optional :All Area Auto Scaling
+ [-RS[cale] ] :Optional :R Scaling
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
>> -I FileFormat
mrc[0] weight[0]
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImageFeatureCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFeatureCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFeatureCalc
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:binary
+ [-o[utput] Out (stdout ).as(outFile::ASCII ) ] :Optional :Output:
+ [-o[utput]GC OutGC (NULL ).as(outFile::mrcImage ) ] :Optional :Output:gc
+ [-o[utput]L[abel] OutLabel (NULL ).as(outFile::mrcImage ) ] :Optional :Output:Label
+ [-o[utput]P[eprimeter]OutPerimeter (NULL ).as(outFile::mrcImage ) ] :Optional :Output:Label
+ [-o[utput]S[urfaceArea]OutSurfaceArea (NULL ).as(outFile::mrcImage ) ] :Optional :Output:SurfaceArea
+ [-n[eighbor] neighbor (0 ).as(Integer ) ] :Optional :Neighbor: [4(0)|8 or 6(0)|18|26]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: mrcImageFeatureExtraction
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[oOccurrence]r[adius]co_r (1 )] :Optional :Co-Occurrence radius
- [-c[oOccurrence]t[heta]co_theta (0 )] :Optional :Co-Occurrence theta
- [-r[unLength]t[heta] rl_theta (0 )] :Optional :RunLength theta
- [-r[unLength]d[ev] rl_dev (4 )] :Optional :RunLength devision
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[oOccurrence]r[adius]co_r (1 ).as(Integer ) ] :Optional :Co-Occurrence radius
+ [-c[oOccurrence]t[heta]co_theta (0 ).as(Integer ) ] :Optional :Co-Occurrence theta
+ [-r[unLength]t[heta] rl_theta (0 ).as(Integer ) ] :Optional :RunLength theta
+ [-r[unLength]d[ev] rl_dev (4 ).as(Integer ) ] :Optional :RunLength devision
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
Feature list
<PRE>
Usage: mrcImageFilterCreate
Options:
- [-i[nput] In (stdin )] :Optional :Input: ASCII
- [-o[utput] Out (stdout )] :Optional :Output: mrcImage
- [-nx Nx (512 )] :Essential :ImageSize: x
- [-ny Ny (512 )] :Optional :ImageSize: y
- [-nz Nz (1 )] :Optional :ImageSize: z
- [-sx Sx (3 )] :Essential :FilterSize: x
- [-sy Sy (3 )] :Optional :FilterSize: y
- [-sz Sz (1 )] :Optional :FilterSize: z
- [-v[erbose] ] :Optional :Verbose
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-M[ode] Mode (0 )] :Optional :Mode: Filter shape
- [-m[ode] mode (2 )] :Optional :mode: output mrc
+ [-i[nput] In (stdin ).as(inFile ) ] :Optional :Input: ASCII
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: mrcImage
+ [-nx Nx (512 ).as(Integer ) ] :Essential :ImageSize: x
+ [-ny Ny (512 ).as(Integer ) ] :Optional :ImageSize: y
+ [-nz Nz (1 ).as(Integer ) ] :Optional :ImageSize: z
+ [-sx Sx (3 ).as(Integer ) ] :Essential :FilterSize: x
+ [-sy Sy (3 ).as(Integer ) ] :Optional :FilterSize: y
+ [-sz Sz (1 ).as(Integer ) ] :Optional :FilterSize: z
+ [-v[erbose] ] :Optional :Verbose
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-M[ode] Mode (0 ).as(Integer ) ] :Optional :Mode: Filter shape
+ [-m[ode] mode (2 ).as(Integer ) ] :Optional :mode: output mrc
----- Additional Usage -----
>>>> Input file Format nx0 y0 z0 weight0
x1 y1 z1 weight1
<PRE>
Usage: mrcImageFilteringbyFile
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-f[ilter] Filter (NULL )] :Essential :FilterFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-f[ilter] Filter (NULL ).as(inFile ) ] :Essential :FilterFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
Mode 0: Filtering input file by filter file.
Mode 1: Output mrc fourier image of filter file.Size of filter is size of input file.
<PRE>
Usage: mrcImageFilteringbyFileForVariance
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-f[ilter] Filter (NULL )] :Essential :FilterFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-f[ilter] Filter (NULL ).as(inFile ) ] :Essential :FilterFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
[-C[enter] Centre (0 ).as(Integer ) ] :Optional :CentreMode
[-M[ode] GetMode (0 ).as(Integer ) ] :Optional :PixelDataGetHowToGet: InterpolationMode
[-FSC ] :Optional :Output:predicted FSC
+ [-Cref ] :Optional :Output:Cref
+ [-FSCfull ] :Optional :Output:FSC full
+ [-NoiseWeighted Brestore (0.0 ).as(Real ) ] :Optional :NoiseWeighted: Cref*exp(-Brestore/(4*d^2)
[-mask InMask (NULL ).as(inFile::mrcImage ) ] :Optional :Input: Mask for FSC
[-maskBack InBackMask (NULL ).as(inFile::mrcImage ) ] :Optional :Input: Mask for FSC Back
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
+0: Centre is ImageCentre Shift: (Nx/2.0, Ny/2.0, Nz/2.0 )
+1: Centre is BottomLeft Shift: (0, 0, 0 )
+2: Use StartN Shift: (StartNx,StartNy,StartNz)
+Duncan Sousa, Nikolaus Grigorieff, 2007, JSB
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageFractalFourierShellCorrelation
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrcImage Input
- [-r[eference] Ref (NULL )] :Essential :Input: mrcImage Reference
- [-o[utput] Out (NULL )] :Essential :Output: ResolutionMap
- [-t[hreshold] Threshold (0.5 )] :Optional :Input: Threshold
- [-s[tep]x stepx (1 )] :Optional :Input: step x
- [-s[tep]y stepy (1 )] :Optional :Input: step y
- [-s[tep]z stepz (1 )] :Optional :Input: step z
- [-maxN maxN (32 )] :Optional :Input: max partIn.HeaderN
- [-scaling[ up] scaling (1.25 )] :Optional :Input: scaling up
- [-get[ mode] getMode (0 )] :Optional :Input:mrcPixelDataGetMode
- [-Log Log (NULL )] :Optional :Output: Log File
- [-xmin xmin (0 )] :Optional :Input: xmin
- [-ymin ymin (0 )] :Optional :Input: ymin
- [-zmin zmin (0 )] :Optional :Input: zmin
- [-xmax xmax (0 )] :Optional :Input: xmax
- [-ymax ymax (0 )] :Optional :Input: ymax
- [-zmax zmax (0 )] :Optional :Input: zmax
- [-d[ensity] densityThreshold (0 )] :Optional :Input: density threshold
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrcImage Input
+ [-r[eference] Ref (NULL ).as(inFile ) ] :Essential :Input: mrcImage Reference
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: ResolutionMap
+ [-t[hreshold] Threshold (0.5 ).as(Real ) ] :Optional :Input: Threshold
+ [-s[tep]x stepx (1 ).as(Real ) ] :Optional :Input: step x
+ [-s[tep]y stepy (1 ).as(Real ) ] :Optional :Input: step y
+ [-s[tep]z stepz (1 ).as(Real ) ] :Optional :Input: step z
+ [-maxN maxN (32 ).as(Real ) ] :Optional :Input: max partIn.HeaderN
+ [-scaling[ up] scaling (1.25 ).as(Real ) ] :Optional :Input: scaling up
+ [-get[ mode] getMode (0 ).as(Integer ) ] :Optional :Input:mrcPixelDataGetMode
+ [-Log Log (NULL ).as(outFile ) ] :Optional :Output: Log File
+ [-xmin xmin (0 ).as(Real ) ] :Optional :Input: xmin
+ [-ymin ymin (0 ).as(Real ) ] :Optional :Input: ymin
+ [-zmin zmin (0 ).as(Real ) ] :Optional :Input: zmin
+ [-xmax xmax (0 ).as(Real ) ] :Optional :Input: xmax
+ [-ymax ymax (0 ).as(Real ) ] :Optional :Input: ymax
+ [-zmax zmax (0 ).as(Real ) ] :Optional :Input: zmax
+ [-d[ensity] densityThreshold (0 ).as(Real ) ] :Optional :Input: density threshold
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageGaussDisc
Options:
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-sigmax sigmax (10 )] :Optional :sigmax[A]
- [-sigmay sigmay (10 )] :Optional :sigmay[A]
- [-sigma_range sigma_range (3 )] :Optional :sigma
- [-weight weight (10 )] :Optional :weight
- [-size size (5 )] :Optional :Pixel Size[A]
- [-W[idth] Width (0 )] :Optional :Image Width[A]
- [-H[eight] Height (0 )] :Optional :Image Height[A]
- [-cx centrex (0 )] :Optional :x: Centre[A]
- [-cy centrey (0 )] :Optional :y: Centre[A]
- [-a[ngle] Angle (0 )] :Optional :Angle: [degree]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (2 )] :Optional :Mode
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-sigmax sigmax (10 ).as(Real ) ] :Optional :sigmax[A]
+ [-sigmay sigmay (10 ).as(Real ) ] :Optional :sigmay[A]
+ [-sigma_range sigma_range (3 ).as(Real ) ] :Optional :sigma
+ [-weight weight (10 ).as(Real ) ] :Optional :weight
+ [-size size (5 ).as(Real ) ] :Optional :Pixel Size[A]
+ [-W[idth] Width (0 ).as(Real ) ] :Optional :Image Width[A]
+ [-H[eight] Height (0 ).as(Real ) ] :Optional :Image Height[A]
+ [-cx centrex (0 ).as(Real ) ] :Optional :x: Centre[A]
+ [-cy centrey (0 ).as(Real ) ] :Optional :y: Centre[A]
+ [-a[ngle] Angle (0 ).as(Real ) ] :Optional :Angle: [degree]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (2 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
Gauss Disc is cutted at sigma_range*sigma
Gauss Disc = weight * exp ( - ((x^2 / sigmax^2)+(y^2 / sigmay^2))
<PRE>
Usage: mrcImageGaussSphere
Options:
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-E[uler]A[ngle] EA (YOYS )Rot1 (0.0 )Rot2 (0.0 )Rot3 (0.0 )] :Optional :Input: Gauss Sphere: Rotation
- [-centre ShiftX (0.0 )ShiftY (0.0 )ShiftZ (0.0 )] :Optional :Input: Gauss Sphere: Centre
- [-sigmax sigmax (10 )] :Optional :sigmax[A]
- [-sigmay sigmay (20 )] :Optional :sigmay[A]
- [-sigmaz sigmaz (30 )] :Optional :sigmaz[A]
- [-sigma_range sigma_range (3 )] :Optional :x times
- [-weight weight (10 )] :Optional :weight
- [-size size (5 )] :Optional :Pixel Size[A]
- [-W[idth] Width (0 )] :Optional :Width[A]
- [-H[ight] Height (0 )] :Optional :Height[A]
- [-S[ection] Section (0 )] :Optional :Section[A]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (2 )] :Optional :Mode
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-E[uler]A[ngle] EA (YOYS ).as(String )
+ Rot1 (0.0 ).as(Real )
+ Rot2 (0.0 ).as(Real )
+ Rot3 (0.0 ).as(Real ) ] :Optional :Input: Gauss Sphere: Rotation
+ [-centre ShiftX (0.0 ).as(Real )
+ ShiftY (0.0 ).as(Real )
+ ShiftZ (0.0 ).as(Real ) ] :Optional :Input: Gauss Sphere: Centre
+ [-sigmax sigmax (10 ).as(Real ) ] :Optional :sigmax[A]
+ [-sigmay sigmay (20 ).as(Real ) ] :Optional :sigmay[A]
+ [-sigmaz sigmaz (30 ).as(Real ) ] :Optional :sigmaz[A]
+ [-sigma_range sigma_range (3 ).as(Real ) ] :Optional :x times
+ [-weight weight (10 ).as(Real ) ] :Optional :weight
+ [-size size (5 ).as(Real ) ] :Optional :Pixel Size[A]
+ [-W[idth] Width (0 ).as(Real ) ] :Optional :Width[A]
+ [-H[ight] Height (0 ).as(Real ) ] :Optional :Height[A]
+ [-S[ection] Section (0 ).as(Real ) ] :Optional :Section[A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (2 ).as(Integer ) ] :Optional :Mode
Gauss Sphere is cutted at sigma_range*sigma
Gauss Sphere = weight * exp ( - ((x^2 / sigmax^2)+(y^2 / sigmay^2)+(z^2 / sigmaz^2))
mrcImageFileSize is (sigma_range*sigmax*2) x (sigma_range*sigmay*2) x (sigma_range*sigmaz*2)
<PRE>
Usage: mrcImageHeaderChange
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[output] Out (NULL )] :Essential :OutputDataFile
- [-r[esolution] r (0.0 )] :Optional :Pixel size
- [-x[length] Lx (0.0 )] :Optional :Pixel size along x axis(A).Default:No change
- [-y[length] Ly (0.0 )] :Optional :Pixel size along y axis(A).Default:No change
- [-z[length] Lz (0.0 )] :Optional :Pixel size along z axis(A).Default:No change
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[output] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-r[esolution] r (0.0 ).as(Real ) ] :Optional :Pixel size
+ [-x[length] Lx (0.0 ).as(Real ) ] :Optional :Pixel size along x axis(A).Default:No change
+ [-y[length] Ly (0.0 ).as(Real ) ] :Optional :Pixel size along y axis(A).Default:No change
+ [-z[length] Lz (0.0 ).as(Real ) ] :Optional :Pixel size along z axis(A).Default:No change
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
If r is defined, pixel size is r
</PRE>
</BODY>
<PRE>
Usage: mrcImageHelicalAveraging
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-dz[deltaz] dz (27.3 )] :Optional :deltaz(A)
- [-dp[deltaphi] dp (-167.143 )] :Optional :deltaphi(degree)
- [-N[umber] N (1 )] :Optional :Number of particles to average
- [-W[indow] W (1 )] :Optional :Window size to average [pixel].
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-dz[deltaz] dz (27.3 ).as(Real ) ] :Optional :deltaz(A)
+ [-dp[deltaphi] dp (-167.143 ).as(Real ) ] :Optional :deltaphi(degree)
+ [-N[umber] N (1 ).as(Integer ) ] :Optional :Number of particles to average
+ [-W[idth] W (1 ).as(Integer ) ] :Optional :Width to average [pixel].
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
0: Discrete. Parameter N is needed.
1: Continuous. Parameter W is needed.
<PRE>
Usage: mrcImageHelicalMappingFrom2DImage
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-Nz Nz (1 )] :Essential :Length of output image (pixel).
- [-dz[deltaz] dz (27.3 )] :Optional :deltaz(A)
- [-dp[deltaphi] dp (-167.143 )] :Optional :deltaphi(degree)
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-Nz Nz (1 ).as(Integer ) ] :Essential :Length of output image (pixel).
+ [-dz[deltaz] dz (27.3 ).as(Real ) ] :Optional :deltaz(A)
+ [-dp[deltaphi] dp (-167.143 ).as(Real ) ] :Optional :deltaphi(degree)
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageHelicalMasking
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-dz[deltaz] dz (27.3 )] :Optional :deltaz(A)
- [-dp[deltaphi] dphi (13.84 )] :Optional :deltaphi(degree)
- [-sz[startz] sz (0 )] :Optional :startz(pixel)
- [-ez[startz] ez (0 )] :Optional :endz(pixel)
- [-sphi[startphi] sphi (0 )] :Optional :startphi(degree) for masking
- [-ephi[startphi] ephi (90 )] :Optional :endphi(degree) for masking
- [-v[alue] value (0 )] :Optional :value to pad
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-dz[deltaz] dz (27.3 ).as(Real ) ] :Optional :deltaz(A)
+ [-dp[deltaphi] dphi (13.84 ).as(Real ) ] :Optional :deltaphi(degree)
+ [-sz[startz] sz (0 ).as(Integer ) ] :Optional :startz(pixel)
+ [-ez[startz] ez (0 ).as(Integer ) ] :Optional :endz(pixel)
+ [-sphi[startphi] sphi (0 ).as(Real ) ] :Optional :startphi(degree) for masking
+ [-ephi[startphi] ephi (90 ).as(Real ) ] :Optional :endphi(degree) for masking
+ [-v[alue] value (0 ).as(Real ) ] :Optional :value to pad
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageHelicalMaskingBy2DImage
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-dz[deltaz] dz (27.3 )] :Optional :deltaz(A)
- [-dp[deltaphi] dphi (13.84 )] :Optional :deltaphi(degree)
- [-M[ask] Mask (NULL )] :Essential :2D Image for masking
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-dz[deltaz] dz (27.3 ).as(Real ) ] :Optional :deltaz(A)
+ [-dp[deltaphi] dphi (13.84 ).as(Real ) ] :Optional :deltaphi(degree)
+ [-M[ask] Mask (NULL ).as(inFile ) ] :Essential :2D Image for masking
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageHelicalProjection
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-dz[deltaz] dz (27.3 )] :Optional :deltaz(A)
- [-dp[deltaphi] dphi (13.84 )] :Optional :deltaphi(degree)
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-dz[deltaz] dz (27.3 ).as(Real ) ] :Optional :deltaz(A)
+ [-dp[deltaphi] dphi (13.84 ).as(Real ) ] :Optional :deltaphi(degree)
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageHighPassFilter
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-h[alf]v[alue]p[oint]hvp (1.0 )] :Optional :HalfValuePoint
- [-p[ath]w[indow] pwLow (0.0 )pwHigh (1.0 )] :Optional :PathWindowWeight: Low <-> High
- [-w[idth] width (1.0 )] :Optional :WidthOfDumping
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-h[alf]v[alue]p[oint]hvp (1.0 ).as(Real ) ] :Optional :HalfValuePoint
+ [-p[ath]w[indow] pwLow (0.0 ).as(Real )
+ pwHigh (1.0 ).as(Real ) ] :Optional :PathWindowWeight: Low <-> High
+ [-w[idth] width (1.0 ).as(Real ) ] :Optional :WidthOfDumping
>>> Mode <<<<
1: Step filter : required argumnent: -hvp
2: Cos filter : required argumnent: -hvp -w
<PRE>
Usage: mrcImageHighlighting
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-b[ias] Bias (0 )] :Optional :BiasValueFromMean
- [-g[rad] Grad (1 )] :Optional :GradientOfFunction
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-b[ias] Bias (0 ).as(Real ) ] :Optional :BiasValueFromMean
+ [-g[rad] Grad (1 ).as(Real ) ] :Optional :GradientOfFunction
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
---- lmrcImageHighlightInfo ----mode: 0:No Operation
1:ArcTan Filter
2:Histgram Equalization
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImageHoughTransform</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageHoughTransform</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageHoughTransform
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output
+ [-d[elta]Theta DeltaTheta (1.0 ).as(Real ) ] :Optional :DeltaTheta[degree]
+ [-d[elta]Rho DeltaRho (1.0 ).as(Real ) ] :Optional :DeltaRho[pixel]
+ [-M[ode] HoughMode (0 ).as(Integer ) ] :Optional :HoughTransformMode
+ [-width widthMin (0 ).as(Real )
+ widthMax (0 ).as(Integer ) ] :Optional :Width[pixel]
+ [-widthOut widthOut (0 ).as(Real ) ] :Optional :Width[pixel]
+ [-I[nterpolation]M[ode]InterpolationMode (0 ).as(Integer ) ] :Optional :mrcImageMode: HowToGet
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+0: Lines
+ 0: Nearest
+ 1: Linear
+1: TwoLines
+ 0: Nearest(centre) + InterpolationMode
+ 1: Linear(centre) + InterpolationMode
+3: Rectangles (not yet)
+4: FilledRectangles (not yet)
+5: Circles (not yet)
+6: FilledCircles (not yet)
+7: GivenStructure (not yet)
+</PRE>
+</BODY>
+</HTML>
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImageHoughTransformInverse</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageHoughTransformInverse</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageHoughTransformInverse
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-Nx Nx (100 ).as(Integer ) ] :Optional :Nx[pixel]
+ [-Ny Ny (100 ).as(Integer ) ] :Optional :Ny[pixel]
+ [-d[elta] delta (1.0 ).as(Integer ) ] :Optional :delta[A]
+ [-M[ode] HoughSpaceMode (0 ).as(Integer ) ] :Optional :HoughMode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
5: mean of Sparse
6: mean of 2DEdge
7: RMS of all pixels
+ 8: sd of all axes
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageInverseRadonTransform
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-Rmax Rmax (1.0 )] :Optional :Input: Rmax
- [-Rmin Rmin (1.0 )] :Optional :Input: Rmin
- [-b[ack]p[rojection]m[ode]BackProjectionMode (1 )] :Optional :BackProjectionMode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-T[hreshold] T (1 )] :Optional :Input: Threshold
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-Rmax Rmax (1.0 ).as(Real ) ] :Optional :Input: Rmax
+ [-Rmin Rmin (1.0 ).as(Real ) ] :Optional :Input: Rmin
+ [-b[ack]p[rojection]m[ode]BackProjectionMode (1 ).as(Integer ) ] :Optional :BackProjectionMode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-T[hreshold] T (1 ).as(Real ) ] :Optional :Input: Threshold
----- BackProjectionMode -----
1 = SimpleBackProjection
<PRE>
Usage: mrcImageLabeling
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-n[eighbor] neighbor (0 ).as(Integer ) ] :Optional :Neighbor[4(0)|8 or 6(0)|18|26]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
+mode: 0 (default: speed)
+ 1 (No vacancy)
</PRE>
</BODY>
</HTML>
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImageLocalMaximumValuesFind</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageLocalMaximumValuesFind</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageLocalMaximumValuesFind
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Optional :OutputDataFile
+ [-O[utput] OutP (stdout ).as(outFile::ASCII ) ] :Optional :OutputDataFile
+ [-T[hreshold] Threshold (0 ).as(Real ) ] :Optional :Threshold
+ [-S[ize] Size (3 ).as(Integer ) ] :Optional :Size
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: mrcImageLowPassFilter
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-h[alf]v[alue]p[oint]hvp (1.0 )] :Optional :HalfValuePoint[/A]
- [-w[idth] width (1.0 )] :Optional :WidthOfDumping
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-h[alf]v[alue]p[oint]hvp (1.0 ).as(Real ) ] :Optional :HalfValuePoint[/A]
+ [-w[idth] width (1.0 ).as(Real ) ] :Optional :WidthOfDumping
>>> Mode <<<<
1: Step filter : required argumnent: -hvp
2: Cos filter : required argumnent: -hvp -w
<PRE>
Usage: mrcImageMagnificationChange
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-r[atio] Ratio (0 )] :Essential :Ratio of new magnification to old magnification
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-r[atio] Ratio (0 ).as(Real ) ] :Essential :Ratio of new magnification to old magnification
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageMake2DArrayImage
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile(Array of input image file)
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-N[umber] Nx (1 )] :Optional :Number of column
- [-w[idth] w (0 )] :Optional :Width of separating line
- [-v[alue] v (0 )] :Optional :Value of separating line
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile(Array of input image file)
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-N[umber] Nx (1 ).as(Integer ) ] :Optional :Number of column
+ [-w[idth] w (0 ).as(Integer ) ] :Optional :Width of separating line
+ [-v[alue] v (0 ).as(Real ) ] :Optional :Value of separating line
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
mode 0:Input is data array.
mode 1:Input is one 3D file.
<PRE>
Usage: mrcImageMakeCylinder
Options:
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-i[nput] In (NULL )] :Optional :InputDataFile
- [-r[esolution] Resolution (1.666666 )] :Optional :Size of pixel[A].
- [-Nx[Number of x] Nx (0 )] :Essential :Number of x
- [-Ny[Number of y] Ny (0 )] :Essential :Number of y
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputDataFile
+ [-r[esolution] Resolution (1.666666 ).as(Real ) ] :Optional :Size of pixel[A].
+ [-Nx[Number of x] Nx (0 ).as(Integer ) ] :Essential :Number of x
+ [-Ny[Number of y] Ny (0 ).as(Integer ) ] :Essential :Number of y
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageMakeDump
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageMakeFromTextFile
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-nx nx (1 )] :Optional :Pixel[Def:]
- [-ny ny (1 )] :Optional :Pixel[Def:]
- [-nz nz (1 )] :Optional :Pixel[Def:]
- [-d d (2.5 )] :Optional :d
- [-v v (0 )] :Optional :default value
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-nx nx (1 ).as(Integer ) ] :Optional :Pixel[Def:]
+ [-ny ny (1 ).as(Integer ) ] :Optional :Pixel[Def:]
+ [-nz nz (1 ).as(Integer ) ] :Optional :Pixel[Def:]
+ [-d d (2.5 ).as(Real ) ] :Optional :d
+ [-v v (0 ).as(Real ) ] :Optional :default value
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageMakeSphere
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile (Template file)
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-C[enter] Cx (0 )Cy (0 )Cz (0 )] :Optional :Cetnter position of Sphere.
- [-or[Outer Radius] or (1 )] :Essential :Outer Radius (pixel)
- [-ir[Inner Radius] ir (0 )] :Optional :Inner Radius (pixel)
- [-r[adius] r (0 )] :Optional :Center Radius (pixel): For mode 1 only.
- [-v[alue] Value (10.0 )] :Optional :Value of sphere
- [-Other Other (NULL )] :Optional :Other acceptors. For FRET Calculation.
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile (Template file)
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-C[enter] Cx (0 ).as(Real )
+ Cy (0 ).as(Real )
+ Cz (0 ).as(Real ) ] :Optional :Cetnter position of Sphere.
+ [-or[Outer Radius] or (1 ).as(Real ) ] :Essential :Outer Radius (pixel)
+ [-ir[Inner Radius] ir (0 ).as(Real ) ] :Optional :Inner Radius (pixel)
+ [-r[adius] r (0 ).as(Real ) ] :Optional :Center Radius (pixel): For mode 1 only.
+ [-v[alue] Value (10.0 ).as(Real ) ] :Optional :Value of sphere
+ [-Other Other (NULL ).as(inFile ) ] :Optional :Other acceptors. For FRET Calculation.
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
mode 0: Constant
mode 1: Gaussian
<PRE>
Usage: mrcImageMappingtoPdb
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputPdbFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-ipdb[file] InPdb (NULL )] :Essential :InputPdbFile
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputPdbFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-ipdb[file] InPdb (NULL ).as(inFile ) ] :Essential :InputPdbFile
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageMasking
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-nx nx (0 )] :Optional :Default:in.HeaderN.x
- [-ny ny (0 )] :Optional :Default:in.HeaderN.y
- [-nz nz (0 )] :Optional :Default:in.HeaderN.z
- [-cx cx (0 )] :Optional :Default:Center of image
- [-cy cy (0 )] :Optional :Default:Center of image
- [-cz cz (0 )] :Optional :Default:Center of image
- [-Rot[ation] Euler (0 )Rot1 (0 )Rot2 (0 )Rot3 (0 )] :Optional :Masking Area Rotation Default: ZONS 0 0 0
- [-Shape Shape (0 )] :Optional :Default:Circle
- [-Normalize Normalize (0 )] :Optional :Default:No Op
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-nx nx (0 ).as(Real ) ] :Optional :Default:in.HeaderN.x
+ [-ny ny (0 ).as(Real ) ] :Optional :Default:in.HeaderN.y
+ [-nz nz (0 ).as(Real ) ] :Optional :Default:in.HeaderN.z
+ [-cx cx (0 ).as(Real ) ] :Optional :Default:Center of image
+ [-cy cy (0 ).as(Real ) ] :Optional :Default:Center of image
+ [-cz cz (0 ).as(Real ) ] :Optional :Default:Center of image
+ [-Rot[ation] Euler (0 ).as(String )
+ Rot1 (0 ).as(Real )
+ Rot2 (0 ).as(Real )
+ Rot3 (0 ).as(Real ) ] :Optional :Masking Area Rotation Default: ZONS 0 0 0
+ [-Shape Shape (0 ).as(Integer ) ] :Optional :Default:Circle
+ [-Normalize Normalize (0 ).as(Integer ) ] :Optional :Default:No Op
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- -Shape Option -----
-Shape 0 : Circle : radius(nx, ny, nz)
-Shape 1 : Square : radius(nx, ny, nz)
<PRE>
Usage: mrcImageMaskingByImage
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-M[askingFile] MaskFile (NULL )] :Essential :FilenameForMasking
- [-v[alueForCut] CutValue (0 )] :Optional :ValueForCut
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-M[askingFile] MaskFile (NULL ).as(inFile ) ] :Essential :FilenameForMasking
+ [-v[alueForCut] CutValue (0 ).as(Real ) ] :Optional :ValueForCut
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
mode = 0 : cut off values larger that CutValue.
mode = 1 : cut off values smaller that CutValue.
mode = 2 : multiplying mask image
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImageMeanFreePathCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageMeanFreePathCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageMeanFreePathCalc
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:mrcImage
+ [-o[utput] Out (stdout ).as(outFile::ASCII ) ] :Optional :Output:distribution
+ [-O[utput]w[hite] OutWhite (NULL ).as(outFile::mrcImage ) ] :Optional :Output: white
+ [-O[utput]b[lack] OutBlack (NULL ).as(outFile::mrcImage ) ] :Optional :Output: black
+ [-O[utput]w[hite]e[dge]OutWhiteEdge (NULL ).as(outFile::mrcImage ) ] :Optional :Output: whiteEdge
+ [-O[utput]b[lack]e[dge]OutBlackEdge (NULL ).as(outFile::mrcImage ) ] :Optional :Output: blackEdge
+ [-l[ine]t[hickness] LineThicknessX (1 ).as(Real )
+ LineThicknessY (1 ).as(Real ) ] :Optional :[pixel]
+ [-l[ine]m[ode] LineMode (0 ).as(Integer ) ] :Optional :LineMode
+ [-l[ine]s[hape] LineShape (0 ).as(Integer ) ] :Optional :LineShape
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+>>>> mode
+0: AlongZ-axis
+1: AlongX-axis
+2: AlongY-axis
++16: Length is shown in real using HeaderLength
+>>>> line shape
+0: LineShape-Rectangle
+1: LineShape-Disk
+>>>> line mode
+0: LineMode-And
+1: LineMode-Or
+2: LineMode-GE(Greater than or equal to)
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: mrcImageMergebyside
Options:
- [-i1[input1] In1 (NULL )] :Essential :InputDataFile
- [-i2[input2] In2 (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-v[alue] sep (0 )] :Optional :Value for separation:For mode 1 only
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i1[input1] In1 (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i2[input2] In2 (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-v[alue] sep (0 ).as(Real ) ] :Optional :Value for separation:For mode 1 only
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageMirroring
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
lmrcImageMirroring >>>> Usage >>>>
0: Mirroing against YZ-plane
<PRE>
Usage: mrcImageModeChange
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-Min Min (0.0 )] :Optional :Min
- [-Max Max (1.0 )] :Optional :Max
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-Min Min (0.0 ).as(Real ) ] :Optional :Min
+ [-Max Max (1.0 ).as(Real ) ] :Optional :Max
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageModelCreate
Options:
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-i[nput] In (NULL )] :Optional :InputDataFile
- [-nx nx (70 )] :Optional :Real length = nx * lx
- [-ny ny (70 )] :Optional :Real length = ny * ly
- [-nz nz (100 )] :Optional :Real lenght = nz * lz
- [-r r (1 )] :Optional :Radius[pixel]
- [-lx lx (5.0 )] :Optional :Pixel Size[Angstrom]
- [-ly ly (5.0 )] :Optional :Pixel Size[Angstrom]
- [-lz lz (5.0 )] :Optional :Pixel Size[Angstrom]
- [-radius radius (150 )] :Optional :filament radius [A]
- [-n nHelix (3 )] :Optional :n-helix
- [-dz zPitch (143 )] :Optional :pitch [A]
- [-dphi deltaPhi (40 )] :Optional :rotation angle [degree]
- [-phi phiAngle (120 )] :Optional :rotation angle in the same level [degree]
- [-sz startZ (0 )] :Optional :start z [A]
- [-ez endZ (500 )] :Optional :end z [A]
- [-sphi startPhi (0 )] :Optional :start angle [degree]
- [-sphi2 startPhi2 (40 )] :Optional :start angle 2 [degree]
- [-inMode inMode (0 )] :Optional :inMode
- [-units units (9 )] :Optional :units number
- [-fm fm (0 )] :Optional :formation
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputDataFile
+ [-nx nx (70 ).as(Integer ) ] :Optional :Real length = nx * lx
+ [-ny ny (70 ).as(Integer ) ] :Optional :Real length = ny * ly
+ [-nz nz (100 ).as(Integer ) ] :Optional :Real lenght = nz * lz
+ [-r r (1 ).as(Integer ) ] :Optional :Radius[pixel]
+ [-l l (1 ).as(Integer ) ] :Optional :Length[pixel]
+ [-lx lx (5.0 ).as(Real ) ] :Optional :Pixel Size[Angstrom]
+ [-ly ly (5.0 ).as(Real ) ] :Optional :Pixel Size[Angstrom]
+ [-lz lz (5.0 ).as(Real ) ] :Optional :Pixel Size[Angstrom]
+ [-radius radius (150 ).as(Real ) ] :Optional :filament radius [A]
+ [-n nHelix (3 ).as(Integer ) ] :Optional :n-helix
+ [-dz zPitch (143 ).as(Real ) ] :Optional :pitch [A]
+ [-dphi deltaPhi (40 ).as(Real ) ] :Optional :rotation angle [degree]
+ [-phi phiAngle (120 ).as(Real ) ] :Optional :rotation angle in the same level [degree]
+ [-sz startZ (0 ).as(Real ) ] :Optional :start z [A]
+ [-ez endZ (500 ).as(Real ) ] :Optional :end z [A]
+ [-sphi startPhi (0 ).as(Real ) ] :Optional :start angle [degree]
+ [-sphi2 startPhi2 (40 ).as(Real ) ] :Optional :start angle 2 [degree]
+ [-inMode inMode (0 ).as(Integer ) ] :Optional :inMode
+ [-units units (9 ).as(Integer ) ] :Optional :units number
+ [-fm fm (0 ).as(Integer ) ] :Optional :formation
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+>>>>
+-nx -ny -nz : image size[pixel]
+-lx -ly -lz : pixel/voxel size[Angstrom]
>>>> Mode <<<< (-m)
0: Circle(a right cylinder:3D) and Triangle(a trigonal prism:3D)
Optional argument : -nx -ny -nz -r
Optional argument : -nx -ny
7: SheppLogan 3D
Optional argument : -nx -ny -nz
+8: Cylinder 3D
+ Optional argument : -nx -ny -nz -r -l
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageModelSubfilamentsCreate
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-nx nx (71 )] :Optional :Real length = nx * lx
- [-ny ny (71 )] :Optional :Real length = ny * ly
- [-nz nz (100 )] :Optional :Real lenght = nz * lz
- [-lx lx (5.0 )] :Optional :Pixel Size[Angstrom]
- [-ly ly (5.0 )] :Optional :Pixel Size[Angstrom]
- [-lz lz (5.0 )] :Optional :Pixel Size[Angstrom]
- [-position position (70 )] :Optional :subfilaments position from center [A]
- [-n nHelix (3 )] :Optional :n-helix
- [-dphi deltaPhi (1.395348837)] :Optional :rotation angle [degree]
- [-sphi startPhi (0 )] :Optional :start angle [degree]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-nx nx (71 ).as(Integer ) ] :Optional :Real length = nx * lx
+ [-ny ny (71 ).as(Integer ) ] :Optional :Real length = ny * ly
+ [-nz nz (100 ).as(Integer ) ] :Optional :Real lenght = nz * lz
+ [-lx lx (5.0 ).as(Real ) ] :Optional :Pixel Size[Angstrom]
+ [-ly ly (5.0 ).as(Real ) ] :Optional :Pixel Size[Angstrom]
+ [-lz lz (5.0 ).as(Real ) ] :Optional :Pixel Size[Angstrom]
+ [-position position (70 ).as(Real ) ] :Optional :subfilaments position from center [A]
+ [-n nHelix (3 ).as(Integer ) ] :Optional :n-helix
+ [-dphi deltaPhi (1.395348837).as(Real ) ] :Optional :rotation angle [degree]
+ [-sphi startPhi (0 ).as(Real ) ] :Optional :start angle [degree]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageMontageCreate
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-nx Nx (10 )] :Optional :Nx: If this option does not set, the default value will be set
- [-ny Ny (10 )] :Optional :Ny: If this option does not set, the value will be set automatically
- [-W[idth] Width (10 )] :Optional :Width: If this option does not set, the value will be set automatically
- [-H[eight] Height (10 )] :Optional :Height: If this option does not set, the value will be set automatically
- [-AW[indow] AvgWnd (2000 )] :Optional :AverageWindow for Pad
- [-V[alue] Value (0.0 )] :Optional :
- [-P[ad]M[ode] PadMode (3 )] :Optional :
- [-EdgeAverage ] :Optional :
- [-EdgeAverageWindow EdgeAverageWindow (4 )] :Optional :Definition of Edge
- [-NoAverage ] :Optional :
- [-Max Max (16383 )] :Optional :MaximumValue: If the pixel value is more than this max, the pixel value is assigned to the Value indicated by -V or -VMax.
- [-VMax VMax (16383 )] :Optional :Attention: related to -Max
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFileListNoOpen ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-nx Nx (10 ).as(Integer ) ] :Optional :Nx: If this option does not set, the default value will be set
+ [-ny Ny (10 ).as(Integer ) ] :Optional :Ny: If this option does not set, the value will be set automatically
+ [-W[idth] Width (10 ).as(Integer ) ] :Optional :Width: If this option does not set, the value will be set automatically
+ [-H[eight] Height (10 ).as(Integer ) ] :Optional :Height: If this option does not set, the value will be set automatically
+ [-AW[indow] AvgWnd (2000 ).as(Real ) ] :Optional :AverageWindow for Pad
+ [-V[alue] Value (0.0 ).as(Real ) ] :Optional :
+ [-P[ad]M[ode] PadMode (3 ).as(Integer ) ] :Optional :
+ [-EdgeAverage ] :Optional :
+ [-EdgeAverageWindow EdgeAverageWindow (4 ).as(Integer ) ] :Optional :Definition of Edge
+ [-NoAverage ] :Optional :
+ [-Max Max (16383 ).as(Real ) ] :Optional :MaximumValue: If the pixel value is more than this max, the pixel value is assigned to the Value indicated by -V or -VMax.
+ [-VMax VMax (16383 ).as(Real ) ] :Optional :Attention: related to -Max
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
>>> -i inputfile <<<: InputFile Format
hf0000.roi
<PRE>
Usage: mrcImageMove
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-x x (0.0 )] :Optional :shift:[pixel]
- [-y y (0.0 )] :Optional :shift:[pixel]
- [-z z (0.0 )] :Optional :shift:[pixel]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-x x (0.0 ).as(Real ) ] :Optional :shift:[pixel]
+ [-y y (0.0 ).as(Real ) ] :Optional :shift:[pixel]
+ [-z z (0.0 ).as(Real ) ] :Optional :shift:[pixel]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
Mode for lmrcImageMove
0: Move following Pixel Unit
<PRE>
Usage: mrcImageMultiCTFDetermination
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (stdout )] :Optional :Output Optimum
- [-oP[utput] Out2 (NULL )] :Optional :Output Distribution
- [-kV kV (200 )] :Optional :AccVol[kV]
- [-Cs Cs (1.7 )] :Optional :Cs[mm]
- [-AoverP minAoverP (0.0 )maxAoverP (1.0 )delAoverP (0.01 )] :Optional :AoverP[A]
- [-Rmax Rmax (0.1 )] :Optional :Rmax[/A]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFileList ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output Optimum
+ [-oP[utput] Out2 (NULL ).as(outFile ) ] :Optional :Output Distribution
+ [-kV kV (200 ).as(Real ) ] :Optional :AccVol[kV]
+ [-Cs Cs (1.7 ).as(Real ) ] :Optional :Cs[mm]
+ [-AoverP minAoverP (0.0 ).as(Real )
+ maxAoverP (1.0 ).as(Real )
+ delAoverP (0.01 ).as(Real ) ] :Optional :AoverP[A]
+ [-Rmax Rmax (0.1 ).as(Real ) ] :Optional :Rmax[/A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
>>>> inputfile format <<<<
filename minDef[A] maxDef[A] deltaDef[A]
<PRE>
Usage: mrcImageMultiplying
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-v[alue] Value (10.0 )] :Optional :mrcImage x value
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-v[alue] Value (10.0 ).as(Real ) ] :Optional :mrcImage x value
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
---- Additional Usage ----
</PRE>
</BODY>
<PRE>
Usage: mrcImageMultiplyingbyFile
Options:
- [-i1[input1] In1 (NULL )] :Optional :InputDataFile1
- [-i2[input2] In2 (NULL )] :Optional :InputDataFile2
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i1[input1] In1 (NULL ).as(inFile ) ] :Optional :InputDataFile1
+ [-i2[input2] In2 (NULL ).as(inFile ) ] :Optional :InputDataFile2
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
-<HTML>
-<HEAD>
-<TITLE>mrcImageNLMeansFilter</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageNLMeansFilter</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageNLMeansFilter
-Options:
- [-i[nput] In (NULL )] :Essential :Input: MRC
- [-o[utput] Out (NULL )] :Essential :Output: MRC
- [-N[size] Nsize (3 )] :Optional :Input: N-size
- [-hParam hParam (0.5 )] :Optional :Input: hParam
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageNLMeansFilter: No such file or directory
<PRE>
Usage: mrcImageNeuralNetParticleLearning
Options:
- [-i[nput]p[ositive] InPositive (NULL )] :Essential :Input: partile image list filename
- [-i[nput]n[egative] InNegative (NULL )] :Essential :Input: background image list filename
- [-o[utput] Out (NULL )] :Essential :Output: Neural Net Parameters after Learning
+ [-i[nput]p[ositive] InPositive (NULL ).as(inFileList ) ] :Essential :Input: partile image list filename
+ [-i[nput]n[egative] InNegative (NULL ).as(inFileList ) ] :Essential :Input: background image list filename
+ [-o[utput] Out (NULL ).as(outFileList ) ] :Essential :Output: Neural Net Parameters after Learning
FileNameOfWeightForTheBelowLayer NumOfCellOfThisLayer BiasOfThisLayer
- [-B[ias0] Bias (1.0 )] :Optional :Bias: The value of the bias of the input layer
- [-max[Counter] MaxCounter (10 )] :Optional :MaxCounter
- [-EPS EPS (0.005 )] :Optional :Final Error
- [-lambda Lambda (0.1 )] :Optional :step for backpropagation
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-B[ias0] Bias (1.0 ).as(Real ) ] :Optional :Bias: The value of the bias of the input layer
+ [-max[Counter] MaxCounter (10 ).as(Integer ) ] :Optional :MaxCounter
+ [-EPS EPS (0.005 ).as(Real ) ] :Optional :Final Error
+ [-lambda Lambda (0.1 ).as(Real ) ] :Optional :step for backpropagation
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageNfoldAxisSearch
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (stdout )] :Optional :Output: centre
- [-O[utput] Out2 (stdout )] :Optional :Output: shifted Image
- [-res[ideu] Res (NULL )] :Optional :OutputDataFile
- [-n[Fold] nFold (2 )] :Essential :Input: nFold
- [-delPHI delPHI (1.0 )] :Optional :Input: delPHI[degree]
- [-rangex minx (-3 )maxx (3 )delx (1 )] :Optional :Input: range [pixel size]
- [-rangey miny (-3 )maxy (3 )dely (1 )] :Optional :Input: range [pixel size]
- [-rangez minz (0 )maxz (0 )delz (1 )] :Optional :Input: range [pixel size]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: centre
+ [-O[utput] Out2 (stdout ).as(outFile ) ] :Optional :Output: shifted Image
+ [-res[ideu] Res (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-n[Fold] nFold (2 ).as(Integer ) ] :Essential :Input: nFold
+ [-delPHI delPHI (1.0 ).as(Real ) ] :Optional :Input: delPHI[degree]
+ [-rangex minx (-3 ).as(Real )
+ maxx (3 ).as(Real )
+ delx (1 ).as(Real ) ] :Optional :Input: range [pixel size]
+ [-rangey miny (-3 ).as(Real )
+ maxy (3 ).as(Real )
+ dely (1 ).as(Real ) ] :Optional :Input: range [pixel size]
+ [-rangez minz (0 ).as(Real )
+ maxz (0 ).as(Real )
+ delz (1 ).as(Real ) ] :Optional :Input: range [pixel size]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageNoiseAdd
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-SD SD (1.0 )] :Optional :SD of Image/Signal
- [-NS NS (1.0 )] :Optional :N/S: Attention:Noise to Signal ratio
- [-SN SN (1.0 )] :Optional :S/N: Signal to Noise ratio
- [-H H (1.0 )] :Optional :High threshold of signal
- [-L L (1.0 )] :Optional :Low threshold of signal
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-SD SD (1.0 ).as(Real ) ] :Optional :SD of Image/Signal
+ [-NS NS (1.0 ).as(Real ) ] :Optional :N/S: Attention:Noise to Signal ratio
+ [-SN SN (1.0 ).as(Real ) ] :Optional :S/N: Signal to Noise ratio
+ [-H H (1.0 ).as(Real ) ] :Optional :High threshold of signal
+ [-L L (1.0 ).as(Real ) ] :Optional :Low threshold of signal
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageNoiseCreate
Options:
- [-r[eference] In (NULL )] :Essential :ReferenceDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-s[tandard deviation]Noise (1.0 )] :Optional :Standard deviation of noise
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-r[eference] In (NULL ).as(inFile ) ] :Essential :ReferenceDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-s[tandard deviation]Noise (1.0 ).as(Real ) ] :Optional :Standard deviation of noise
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
Output file has the same infomation (Nx Ny Nz Length and so on) as reference file.
</PRE>
<PRE>
Usage: mrcImageNoiseReductionByRelaxation
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-n[umber] Nlab (8 )] :Optional :Number of Density Level
- [-max[imum] max (0 )] :Optional :Maximum of Density Level
- [-min[imum] min (0 )] :Optional :Minimum of Density Level
- [-m[ode]1 mode1 (1 )] :Optional :Dij Modeof Personal Style
- [-m[ode]2 mode2 (1 )] :Optional :Dij Mode of Figure Style
- [-m[ode]3 mode3 (1 )] :Optional :Dij Mode of Dimension Style
- [-o[ptional]m[ode] omode (0 )] :Optional :Optional Mode of Noise Reduction
- [-t[imes] times (1 )] :Optional :Times of NoiseReduction
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-n[umber] Nlab (8 ).as(Integer ) ] :Optional :Number of Density Level
+ [-max[imum] max (0 ).as(Integer ) ] :Optional :Maximum of Density Level
+ [-min[imum] min (0 ).as(Integer ) ] :Optional :Minimum of Density Level
+ [-m[ode]1 mode1 (1 ).as(Integer ) ] :Optional :Dij Modeof Personal Style
+ [-m[ode]2 mode2 (1 ).as(Integer ) ] :Optional :Dij Mode of Figure Style
+ [-m[ode]3 mode3 (1 ).as(Integer ) ] :Optional :Dij Mode of Dimension Style
+ [-o[ptional]m[ode] omode (0 ).as(Integer ) ] :Optional :Optional Mode of Noise Reduction
+ [-t[imes] times (1 ).as(Integer ) ] :Optional :Times of NoiseReduction
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageNormalizedSubtraction
Options:
- [-i1[nput] In1 (NULL )] :Essential :InputDataFile
- [-i2[nput] In2 (NULL )] :Essential :InputDataFile
- [-nori2[nput] In2_tmp (NULL )] :Optional :OutDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-rmsd RMSD (stdout )] :Optional :Output: RMSD
- [-p[rameter]f[ile] ParamFile (stdout )] :Optional :ParameterOutputFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i1[nput] In1 (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i2[nput] In2 (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-nori2[nput] In2_tmp (NULL ).as(outFile ) ] :Optional :OutDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-rmsd RMSD (stdout ).as(outFile ) ] :Optional :Output: RMSD
+ [-p[rameter]f[ile] ParamFile (stdout ).as(outFile ) ] :Optional :ParameterOutputFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
-- Attention ---
-in1(default) - in2(normalized) :
+in1(default:ref) - in2(normalized:tst) :
-- Mode ---
1: Sigma!=1.0
2: Stdout
<PRE>
Usage: mrcImageNormalizing
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-A A (1.0 )] :Optional :A
- [-B B (0.0 )] :Optional :B
- [-ContourMin ContourMin (0.0 )] :Optional :ContourMin
- [-ContourMax ContourMax (1.0 )] :Optional :ContourMax
- [-ContourSolvent ContourSolvent (0.0 )] :Optional :ContourSolvent
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-A A (1.0 ).as(Real ) ] :Optional :A
+ [-B B (0.0 ).as(Real ) ] :Optional :B
+ [-ContourMin ContourMin (0.0 ).as(Real ) ] :Optional :ContourMin
+ [-ContourMax ContourMax (1.0 ).as(Real ) ] :Optional :ContourMax
+ [-ContourSolvent ContourSolvent (0.0 ).as(Real ) ] :Optional :ContourSolvent
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- mode -----
----- Mode for lmrcImageNormalizing -----
0: Double Exponential: Solvent and Object
<PRE>
Usage: mrcImageNullImageCreate
Options:
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-Nx[Number of x] Nx (0 )] :Optional :Nx:Default Nx of inputfile
- [-Ny[Number of y] Ny (0 )] :Optional :Ny:Default Ny of inputfile
- [-Nz[Number of z] Nz (0 )] :Optional :Nz:Default Nz of inputfile
- [-v[alue] Value (0.0 )] :Optional :Value of pixel
- [-d[elta] d (0.0 )] :Optional :Pixel size
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :OutputDataFile
+ [-r[eference] Ref (NULL ).as(inFile::mrcImage ) ] :Optional :Input: Reference Header
+ [-Nx[Number of x] Nx (0 ).as(Integer ) ] :Optional :Nx:Default Nx of inputfile
+ [-Ny[Number of y] Ny (0 ).as(Integer ) ] :Optional :Ny:Default Ny of inputfile
+ [-Nz[Number of z] Nz (0 ).as(Integer ) ] :Optional :Nz:Default Nz of inputfile
+ [-v[alue] Value (0.0 ).as(Real ) ] :Optional :Value of pixel
+ [-d[elta] d (0.0 ).as(Real ) ] :Optional :Pixel size
+ [-M[ode] Mode (2 ).as(Integer ) ] :Optional :ImageMode: 0 char 1 short 2 Float
+ [-Def[ault] ] :Optional :DefaultFixedValueSet
+ [-c[onfig] configFile (NULL ).as(inFile::ASCII ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
+-r is used to define a reference header.
+-Nx etc. are used preferentially.
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageOddBoxel
Options:
- [-I[nput array of file]In (stdin )] :Essential :InputDataFiles
- [-Iter[ation] ] :Optional :IterationFlag
- [-M[olecularWeight] MolecularWeight (1.0 )] :Optional :MolecularWeight (for iteration only)
- [-n[Molecule] nMolecule (1.0 )] :Optional :NumberOfMolecule (for iteration only)
- [-Boxel Boxel (0 )] :Optional :Final volume for iteration uning boxel unit.
- [-d[ensty] Density (1.35 )] :Optional :Density (for iteration only)
- [-I[nverse] ] :Optional :Inverse (for iteration only)
- [-Abs[olute] ] :Optional :AbsoluteFlag
- [-Th[reshold] Th (0.0 )] :Optional :Threshold for calculation. (for iteration only)
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-I[nput array of file]In (stdin ).as(inFileListNoOpen ) ] :Essential :InputDataFiles
+ [-Iter[ation] ] :Optional :IterationFlag
+ [-M[olecularWeight] MolecularWeight (1.0 ).as(Real ) ] :Optional :MolecularWeight (for iteration only)
+ [-n[Molecule] nMolecule (1.0 ).as(Real ) ] :Optional :NumberOfMolecule (for iteration only)
+ [-Boxel Boxel (0 ).as(Integer ) ] :Optional :Final volume for iteration uning boxel unit.
+ [-d[ensty] Density (1.35 ).as(Real ) ] :Optional :Density (for iteration only)
+ [-I[nverse] ] :Optional :Inverse (for iteration only)
+ [-Abs[olute] ] :Optional :AbsoluteFlag
+ [-Th[reshold] Th (0.0 ).as(Real ) ] :Optional :Threshold for calculation. (for iteration only)
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageOneLineSimilarityCalc
Options:
- [-i1[nput] In1 (NULL )] :Essential :InputDataFile
- [-i2[nput] In2 (NULL )] :Essential :InputDataFile
- [-sm[ode] shiftflag (0 )] :Optional :Shift mode
- [-v[alue] value (0 )] :Optional :Optional value of shift
- [-mm[ode] methodmode (0 )] :Optional :Method mode
+ [-i1[nput] In1 (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i2[nput] In2 (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-sm[ode] shiftflag (0 ).as(Integer ) ] :Optional :Shift mode
+ [-v[alue] value (0 ).as(Integer ) ] :Optional :Optional value of shift
+ [-mm[ode] methodmode (0 ).as(Integer ) ] :Optional :Method mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageOpening
Options:
- [-i[nput] In (NULL )] :Essential :Input: MRC
- [-o[utput] Out (NULL )] :Essential :Output: MRC
- [-times times (1 )] :Optional :Times: erosion*times -> dilation*times
- [-o[utput]SE OutSE (NULL )] :Optional :Output: MRC(SE)
- [-S[tructuring]E[lement]SEmode (0 )] :Optional :StructuringElement
- [-r[adius] radius (2 )] :Optional :Radius
- [-n n (5 )] :Optional :size
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: MRC
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: MRC
+ [-times times (1 ).as(Integer ) ] :Optional :Times: erosion*times -> dilation*times
+ [-o[utput]SE OutSE (NULL ).as(outFile ) ] :Optional :Output: MRC(SE)
+ [-S[tructuring]E[lement]SEmode (0 ).as(Integer ) ] :Optional :StructuringElement
+ [-r[adius] radius (2 ).as(Integer ) ] :Optional :Radius
+ [-n n (5 ).as(Integer ) ] :Optional :size
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- Structuring Element : Mode
0: 2D Cross3x3: 4-neighbour
1: 2D Square3x3: 8-neighbour
-2: 2D Open Disk , need (radius, n)
+2: 2D Disk , need (radius, n(squre size))
3: 3D Cross3x3x3: 6-neighbour
4: 3D Cubic3x3x3: 26-neighbour
-5: 3D Open Disk , need (radius, n)
+5: 3D Sphere, need (radius, n(cubic size))
+6: 2D Rectangle, need nx, ny
+7: 3D Cuboid, need nx, ny, nz
+8: 3D Cylindar, need r, nx, ny, nz
-----
Dilation: Max for image : Or for binary image
Erosion: Min for image : And for binary image
<PRE>
Usage: mrcImageOrientationSearchByHigherSelection
Options:
- [-I[nputFileList] In (NULL )] :Essential :InputDataFileList
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-n[umber] n (10 )] :Optional :Number of selection
+ [-I[nputFileList] In (NULL ).as(inFileListNoOpen ) ] :Essential :InputDataFileList
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-n[umber] n (10 ).as(Integer ) ] :Optional :Number of selection
----- Input file format -----
filename LminAve
<PRE>
Usage: mrcImageOrientationSearchByHybridization
Options:
- [-I[nputFileLiest] In (NULL )] :Essential :InputDataFileList
- [-o[utput] Out (NULL )] :Essential :OutputDataFileHeader
- [-e[xtension] extension (NULL )] :Essential :OutputDataFileExtension
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-i[ncrease]r[ate] ir (1 )] :Optional :IncreaseRate
- [-h[ybridization]p[oint]n[umber]hpn (1 )] :Optional :HybridizationPointNumber
- [-m[ode]s[election] ms (0 )] :Optional :ModeOfSelection
- [-i[nitial]r[andom]d[ata]ird (0 )] :Optional :InitialRandomData
+ [-I[nputFileLiest] In (NULL ).as(inFileListNoOpen ) ] :Essential :InputDataFileList
+ [-o[utput] Out (NULL ).as(String ) ] :Essential :OutputDataFileHeader
+ [-e[xtension] extension (NULL ).as(String ) ] :Essential :OutputDataFileExtension
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-i[ncrease]r[ate] ir (1 ).as(Integer ) ] :Optional :IncreaseRate
+ [-h[ybridization]p[oint]n[umber]hpn (1 ).as(Integer ) ] :Optional :HybridizationPointNumber
+ [-m[ode]s[election] ms (0 ).as(Integer ) ] :Optional :ModeOfSelection
+ [-i[nitial]r[andom]d[ata]ird (0 ).as(Integer ) ] :Optional :InitialRandomData
>> This algrithm use results of mrcImageOrientationSearchBySimultaneousMinimization
<PRE>
Usage: mrcImageOrientationSearchBySimultaneousMinimization
Options:
- [-I[nputFileList] In (NULL )] :Essential :InputDataFileList
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-dt[heta] dtheta (1 )] :Optional :dtheta
- [-dp[si] dpsi (1 )] :Optional :dpsi
- [-m[odeof]s[election]ms (0 )] :Optional :modeofselection
- [-i[nitial]r[andom]d[ata]ird (1 )] :Optional :InitialRandomData
- [-M[ax]C[ount] MC (100 )] :Optional :MaxCount
- [-F[ileName]H[eader] FileNameHeader (EulerAngle)] :Optional :FileNameHeader
- [-m[odeof]i[nitial]d[ada]mid (0 )] :Optional :modeofinitialdata
- [-i[nputFile]i[nitial]d[ata]InInitial (NULL )] :Optional :InputDataFileOfInitialData
- [-m[odeof]s[tart]p[oint]msp (0 )] :Optional :mode of start point
- [-m[odeof]a[ngular]a[rea]maa (0 )] :Optional :mode of angular area
- [-p[revious]dt[heta] pdtheta (0 )] :Optional :previous dtheta
- [-p[revious]dp[si] pdpsi (0 )] :Optional :previous dpsi
- [-m[ode]L[calculation]modeL (0 )] :Optional :Mode of L calculation
- [-m[ode]T[hreshold]A[ngularweight]modeTA (0 )] :Optional :Mode of Threshold of AngularWeight
- [-m[ode]c[alculation]a[rea]modeCA (0 )] :Optional :mode of Lvalue of calculation area
- [-t[hreshold]c[alculation]a[rea]TCA (0 )] :Optional :Threshold of Lvalue of calculation area
- [-m[ode]f[ix] modeF (0 )] :Optional :mode of fix
+ [-I[nputFileList] In (NULL ).as(inFileListNoOpen ) ] :Essential :InputDataFileList
+ [-o[utput] Out (NULL ).as(outFileNoOpen ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-dt[heta] dtheta (1 ).as(Real ) ] :Optional :dtheta
+ [-dp[si] dpsi (1 ).as(Real ) ] :Optional :dpsi
+ [-m[odeof]s[election]ms (0 ).as(Integer ) ] :Optional :modeofselection
+ [-i[nitial]r[andom]d[ata]ird (1 ).as(Integer ) ] :Optional :InitialRandomData
+ [-M[ax]C[ount] MC (100 ).as(Integer ) ] :Optional :MaxCount
+ [-F[ileName]H[eader] FileNameHeader (EulerAngle).as(String ) ] :Optional :FileNameHeader
+ [-m[odeof]i[nitial]d[ada]mid (0 ).as(Integer ) ] :Optional :modeofinitialdata
+ [-i[nputFile]i[nitial]d[ata]InInitial (NULL ).as(inFile ) ] :Optional :InputDataFileOfInitialData
+ [-m[odeof]s[tart]p[oint]msp (0 ).as(Integer ) ] :Optional :mode of start point
+ [-m[odeof]a[ngular]a[rea]maa (0 ).as(Integer ) ] :Optional :mode of angular area
+ [-p[revious]dt[heta] pdtheta (0 ).as(Integer ) ] :Optional :previous dtheta
+ [-p[revious]dp[si] pdpsi (0 ).as(Integer ) ] :Optional :previous dpsi
+ [-m[ode]L[calculation]modeL (0 ).as(Integer ) ] :Optional :Mode of L calculation
+ [-m[ode]T[hreshold]A[ngularweight]modeTA (0 ).as(Integer ) ] :Optional :Mode of Threshold of AngularWeight
+ [-m[ode]c[alculation]a[rea]modeCA (0 ).as(Integer ) ] :Optional :mode of Lvalue of calculation area
+ [-t[hreshold]c[alculation]a[rea]TCA (0 ).as(Real ) ] :Optional :Threshold of Lvalue of calculation area
+ [-m[ode]f[ix] modeF (0 ).as(Integer ) ] :Optional :mode of fix
----- ModeSelection -----
-ms : 0 : random
<PRE>
Usage: mrcImagePCA
Options:
- [-i[nput] InList (NULL )] :Essential :Input: filelist
- [-o[utput] OutList (NULL )] :Essential :Output: filelist
- [-EPS EPS (1e2 )] :Optional :EPS: lambda<EPS, stop calculation.
- [-NX NX (30 )] :Optional :NX: pixcelNX
- [-NY NY (30 )] :Optional :NY: pixcelNX
- [-O[utput] Outvector (NULL )] :Optional :Output: vectorfile
- [-EPSO[utput] EPSOutcaletime (NULL )] :Optional :EPSOutput: caletimefile
- [-E[igenImage] EigenImage (eigen )] :Optional :Output: eigenImage
- [-numE[igenImage] numOfEigenImage (10 )] :Optional :Number of eigenImages
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] InList (NULL ).as(inFileListNoOpen ) ] :Essential :Input: filelist
+ [-o[utput] OutList (NULL ).as(outFileListNoOpen ) ] :Essential :Output: filelist
+ [-EPS EPS (1e2 ).as(Real ) ] :Optional :EPS: lambda<EPS, stop calculation.
+ [-NX NX (30 ).as(Integer ) ] :Optional :NX: pixcelNX
+ [-NY NY (30 ).as(Integer ) ] :Optional :NY: pixcelNX
+ [-O[utput] Outvector (NULL ).as(outFile ) ] :Optional :Output: vectorfile
+ [-EPSO[utput] EPSOutcaletime (NULL ).as(outFile ) ] :Optional :EPSOutput: caletimefile
+ [-E[igenImage] EigenImage (eigen ).as(String ) ] :Optional :Output: eigenImage
+ [-numE[igenImage] numOfEigenImage (10 ).as(Integer ) ] :Optional :Number of eigenImages
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImagePad
Options:
- [-i[nput] In (NULL )] :Essential :Input DataFile
- [-o[utput] Out (NULL )] :Essential :Output DataFile
- [-W[idth] Width (0 )] :Optional :Width[pixel]
- [-H[eight] Height (0 )] :Optional :Height[pixel]
- [-V[alue] Value (0.0 )] :Optional :Padding Value(float on avgrage density)
- [-E[xpected]V[alue] ExpectedValue (0.0 )] :Optional :Expected Value for Background
- [-AW AvgWnd (2000.0 )] :Optional :Averaging Window Size [A]
- [-AWMin AWMin (20 )] :Optional :Averaging Window Size[pixel]
- [-AWMax AWMax (22 )] :Optional :Averaging Window Size[pixel]
- [-Tilt TiltAxisAngle (0 )TiltAngle (0 )] :Optional :TiltImage: TiltAxisAngle TiltAngle
- [-c[onfig] configFile (NULL )] :Optional :Configuration File
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input DataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output DataFile
+ [-W[idth] Width (0 ).as(Integer ) ] :Optional :Width[pixel]
+ [-H[eight] Height (0 ).as(Integer ) ] :Optional :Height[pixel]
+ [-V[alue] Value (0.0 ).as(Real ) ] :Optional :Padding Value(float on avgrage density)
+ [-E[xpected]V[alue] ExpectedValue (0.0 ).as(Real ) ] :Optional :Expected Value for Background
+ [-AW AvgWnd (2000.0 ).as(Real ) ] :Optional :Averaging Window Size [A]
+ [-AWMin AWMin (20 ).as(Real ) ] :Optional :Averaging Window Size[pixel]
+ [-AWMax AWMax (22 ).as(Real ) ] :Optional :Averaging Window Size[pixel]
+ [-Tilt TiltAxisAngle (0 ).as(Real )
+ TiltAngle (0 ).as(Real ) ] :Optional :TiltImage: TiltAxisAngle TiltAngle
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :Configuration File
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Mode -----
0: Pad average density(Image Center)
1: Pad average density of x=0 and x=MAX(x)(Image Center)
<PRE>
Usage: mrcImagePanoramaCreate
Options:
- [-I[nput] In (stdin )] :Essential :Input:FileList[mrcImage x y z]
- [-o[utput] Out (NULL )] :Essential :Output:mrcImage
- [-o[utput]C[ount] Count (NULL )] :Optional :Output(Count):mrcImage
- [-N Nx (0 )Ny (0 )Nz (0 )] :Optional :Input:OutImageSize
- [-M[ode] InterpolationMode (0 )] :Optional :InterpolationMode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-I[nput] In (stdin ).as(inFileList ) ] :Essential :Input:FileList[mrcImage x y z]
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output:mrcImage
+ [-o[utput]C[ount] Count (NULL ).as(outFile ) ] :Optional :Output(Count):mrcImage
+ [-N Nx (0 ).as(Integer )
+ Ny (0 ).as(Integer )
+ Nz (0 ).as(Integer ) ] :Optional :Input:OutImageSize
+ [-M[ode] InterpolationMode (0 ).as(Integer ) ] :Optional :InterpolationMode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
>>>InputFileList Format
FileName OffsetX OffsetY OffsetZ
<PRE>
Usage: mrcImageParticleCandidateExtract
Options:
- [-i[nput] In (NULL )] :Essential :Input: MRC
- [-o[utput] Out (NULL )] :Essential :Output: MRC
- [-R[ing]R[adius] RingRadius (100.0 )] :Optional :Input: [A]
- [-R[ing]W[idth] RingWidth (10.0 )] :Optional :Input: [A]
- [-thres[hold] Threshold (3.0 )] :Optional :Input: threshold of IQ
- [-out[Threshold] outFileThres (stdout )] :Optional :Output: Output
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: MRC
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: MRC
+ [-R[ing]R[adius] RingRadius (100.0 ).as(Real ) ] :Optional :Input: [A]
+ [-R[ing]W[idth] RingWidth (10.0 ).as(Real ) ] :Optional :Input: [A]
+ [-thres[hold] Threshold (3.0 ).as(Real ) ] :Optional :Input: threshold of IQ
+ [-out[Threshold] outFileThres (stdout ).as(outFile ) ] :Optional :Output: Output
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImagePattersonFunctionCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImagePattersonFunctionCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImagePattersonFunctionCalc
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:mrcImage
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output:mrcImage
+ [-O[utput] OutPat (stdout ).as(outFile::ASCII ) ] :Optional :Output:ASCII
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: mrcImagePeakSearch
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrcImage
- [-o[utput] Out (NULL )] :Optional :Output: mrcImage
- [-o[utput]B OutB (NULL )] :Optional :Output: mrcImage:Binary
- [-o[utput]L OutL (NULL )] :Optional :Output: mrcImage:Label
- [-o[utput]A OutA (NULL )] :Optional :Output: mrcImage:Aarea
- [-O[utputPeakStatics]OutStatics (stdout )] :Optional :Output as ASCII: Peak statics
- [-t[hreshold] Sigma (3.0 )] :Optional :Input: Peak's values are more than t*sigma.
- [-T[hreshold] Threshold (0.0 )] :Optional :Input: Peak's values are more than T.
- [-a[rea] Area (6.0 )] :Optional :Input[A^2]: Peak's area are more than a.
- [-A[rea] AreaPixel (9 )] :Optional :Input[pixel^2]: Peak's area are more than A.
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrcImage
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :Output: mrcImage
+ [-o[utput]B OutB (NULL ).as(outFile ) ] :Optional :Output: mrcImage:Binary
+ [-o[utput]L OutL (NULL ).as(outFile ) ] :Optional :Output: mrcImage:Label
+ [-o[utput]A OutA (NULL ).as(outFile ) ] :Optional :Output: mrcImage:Aarea
+ [-O[utputPeakStatics]OutStatics (stdout ).as(outFile ) ] :Optional :Output as ASCII: Peak statics
+ [-t[hreshold] Sigma (3.0 ).as(Real ) ] :Optional :Input: Peak's values are more than t*sigma.
+ [-T[hreshold] Threshold (0.0 ).as(Real ) ] :Optional :Input: Peak's values are more than T.
+ [-a[rea] Area (6.0 ).as(Real ) ] :Optional :Input[A^2]: Peak's area are more than a.
+ [-A[rea] AreaPixel (9 ).as(Real ) ] :Optional :Input[pixel^2]: Peak's area are more than A.
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImagePerimeterCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImagePerimeterCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImagePerimeterCalc
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input(Binary)
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output
+ [-o[utput]A[rea] OutArea (NULL ).as(outFile::mrcImage ) ] :Optional :Output
+ [-o[utput]C[hainCode]OutChainCode (NULL ).as(outFile::mrcImage ) ] :Optional :Output
+ [-o[utput]L[abel] OutLabel (NULL ).as(outFile::mrcImage ) ] :Optional :Output
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+>> mode
+ 0: 8-neighbor, chainCode absolute
+ 1: 4-neighbor, chainCode absolute
+ 2: 8-neighbor, chainCode relative
+ 3: 4-neighbor, chainCode relative
+ </PRE>
+</BODY>
+</HTML>
<PRE>
Usage: mrcImagePhaseCTFCompensationFromCTFINFO
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImagePolyROI
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImagePosterization
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-g[radation] Grad (16 )] :Optional :gradation level
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-g[radation] Grad (16 ).as(Integer ) ] :Optional :gradation level
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImagePrint
Options:
- [-i[nput] In (NULL )] :Essential :InputImageFile
- [-o[utput] Out (stdout )] :Optional :OutputImageFile
- [-H[ighThreshold] thresHigh (0.0 )] :Optional :High Threshold
- [-L[owThreshold] thresLow (1.0 )] :Optional :Low Threshold
- [-Section section (z )] :Optional :[z|x|y]Section: Def: z-section
- [-x[Section] xMin (0 )xMax (0 )] :Optional :x section
- [-y[Section] yMin (0 )yMax (0 )] :Optional :y section
- [-z[Section] zMin (0 )zMax (0 )] :Optional :z section
- [-S[cale] Scale (1.0 )] :Optional :Scale(Centre is Bottom Left): -S 1 := 1 mm/pixel
- [-A[bsolute]S[cale] AbScale (1.0 )] :Optional :Scale(Centre is Bottom Left): -AS 1 := 1 mm/A (Real) or 1 mm/A-1 (Fourier Space)
- [-E[nlarge] Enlarge (1.0 )] :Optional :Enlargement(image center is center)
- [-center cx (0.0/* in case of FT or N.x/2.0 in case of Image*/)cy (0.0/* in case of FT or N.y/2.0 in case of Image */)] :Optional :Center of a printed image
- [-C[ontour] contourLevel (1.0 )... ] :Variable :ContourLevel
- [-I[nverse] ] :Optional :Black is High Density.
- [-A[uto] ] :Optional :HighThres=Mean-SD, LowThres=Mean+SD
- [-AC[ontour] AutoContour (10 )] :Optional :Auto Contour(thresHigh <-> mean)
- [-PC[ontour] PeakContour (10 )] :Optional :Peak Contour(thresHigh <-> (mean+thresHigh)/2
- [-AC[ontour]2 AutoContour2 (10 )] :Optional :Auto Contour2(thresHigh <-> thresLow)
- [-Y[expand] Yexpand (1 )] :Optional :Y-axis expanding
- [-RGB Red (0 )Green (0 )Blue (0 )] :Optional :Contour Color Mode: RGB
- [-RGBGradient RedFirst (0 )GreenFirst (0 )BlueFirst (0 )RedLast (0 )GreenLast (0 )BlueLast (0 )] :Optional :Contour Color GradientMode: RGB
- [-HSB Hue (0 )Saturation (0 )Brightness (0 )] :Optional :Contour Color Mode: HSB
- [-HSBGradient HueFirst (0 )SaturationFirst (0 )BrightnessFirst (0 )HueLast (0 )SaturationLast (0 )BrightnessLast (0 )] :Optional :Contour Color GradientMode: HSB
- [-LineColourRGB LineRed (0 )LineGreen (0 )LineBlue (0 )] :Optional :Contour Color Mode: RGB
- [-LineColourRGBGradientLineRedFirst (0 )LineGreenFirst (0 )LineBlueFirst (0 )LineRedLast (0 )LineGreenLast (0 )LineBlueLast (0 )] :Optional :Contour Color GradientMode: RGB
- [-LineColourHSB LineHue (0 )LineSaturation (0 )LineBrightness (0 )] :Optional :Contour Color Mode: HSB
- [-LineColourHSBGradientLineHueFirst (0 )LineSaturationFirst (0 )LineBrightnessFirst (0 )LineHueLast (0 )LineSaturationLast (0 )LineBrightnessLast (0 )] :Optional :Contour Color GradientMode: HSB
- [-LineChange LineColorChange (0.1 )] :Optional :Contour Color Change
- [-LineWidthStart LineWidthStart (0.1 )] :Optional :Contour Line Width Step
- [-LineWidthStep LineWidthStep (0.05 )] :Optional :Contour Line Width Step
- [-ReverseOrder ] :Optional :Reverse Print Order
- [-Untwist untwist (0.0 )] :Optional :Untwist Angle [degree/A], example: (-13,28) = 0.4709576
- [-UpsideDown ] :Optional :Upside Down
- [-Centre ] :Optional :Image Centre is at the centre of paper.
- [-CircleRadius CircleRadius (0.5 )] :Optional :Radius of circles in the case of imageCircles
- [-m[ode] mode (49 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputImageFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputImageFile
+ [-H[ighThreshold] thresHigh (0.0 ).as(Real ) ] :Optional :High Threshold
+ [-L[owThreshold] thresLow (1.0 ).as(Real ) ] :Optional :Low Threshold
+ [-Section section (z ).as(Character ) ] :Optional :[z|x|y]Section: Def: z-section
+ [-x[Section] xMin (0 ).as(Integer )
+ xMax (0 ).as(Integer ) ] :Optional :x section
+ [-y[Section] yMin (0 ).as(Integer )
+ yMax (0 ).as(Integer ) ] :Optional :y section
+ [-z[Section] zMin (0 ).as(Integer )
+ zMax (0 ).as(Integer ) ] :Optional :z section
+ [-S[cale] Scale (1.0 ).as(Real ) ] :Optional :Scale(Centre is Bottom Left): -S 1 := 1 mm/pixel
+ [-A[bsolute]S[cale] AbScale (1.0 ).as(Real ) ] :Optional :Scale(Centre is Bottom Left): -AS 1 := 1 mm/A (Real) or 1 mm/A-1 (Fourier Space)
+ [-E[nlarge] Enlarge (1.0 ).as(Real ) ] :Optional :Enlargement(image center is center)
+ [-center cx (0.0/* in case of FT or N.x/2.0 in case of Image*/).as(Real )
+ cy (0.0/* in case of FT or N.y/2.0 in case of Image */).as(Real ) ] :Optional :Center of a printed image
+ [-C[ontour] contourLevel (1.0 ).as(Real ) ... ] :Variable :ContourLevel
+ [-I[nverse] ] :Optional :Black is High Density.
+ [-A[uto] ] :Optional :HighThres=Mean-SD, LowThres=Mean+SD
+ [-AC[ontour] AutoContour (10 ).as(Integer ) ] :Optional :Auto Contour(thresHigh <-> mean)
+ [-PC[ontour] PeakContour (10 ).as(Integer ) ] :Optional :Peak Contour(thresHigh <-> (mean+thresHigh)/2
+ [-AC[ontour]2 AutoContour2 (10 ).as(Integer ) ] :Optional :Auto Contour2(thresHigh <-> thresLow)
+ [-Y[expand] Yexpand (1 ).as(Real ) ] :Optional :Y-axis expanding
+ [-RGB Red (0 ).as(Real )
+ Green (0 ).as(Real )
+ Blue (0 ).as(Real ) ] :Optional :Contour Color Mode: RGB
+ [-RGBGradient RedFirst (0 ).as(Real )
+ GreenFirst (0 ).as(Real )
+ BlueFirst (0 ).as(Real )
+ RedLast (0 ).as(Real )
+ GreenLast (0 ).as(Real )
+ BlueLast (0 ).as(Real ) ] :Optional :Contour Color GradientMode: RGB
+ [-HSB Hue (0 ).as(Real )
+ Saturation (0 ).as(Real )
+ Brightness (0 ).as(Real ) ] :Optional :Contour Color Mode: HSB
+ [-HSBGradient HueFirst (0 ).as(Real )
+ SaturationFirst (0 ).as(Real )
+ BrightnessFirst (0 ).as(Real )
+ HueLast (0 ).as(Real )
+ SaturationLast (0 ).as(Real )
+ BrightnessLast (0 ).as(Real ) ] :Optional :Contour Color GradientMode: HSB
+ [-LineColourRGB LineRed (0 ).as(Real )
+ LineGreen (0 ).as(Real )
+ LineBlue (0 ).as(Real ) ] :Optional :Contour Color Mode: RGB
+ [-LineColourRGBGradientLineRedFirst (0 ).as(Real )
+ LineGreenFirst (0 ).as(Real )
+ LineBlueFirst (0 ).as(Real )
+ LineRedLast (0 ).as(Real )
+ LineGreenLast (0 ).as(Real )
+ LineBlueLast (0 ).as(Real ) ] :Optional :Contour Color GradientMode: RGB
+ [-LineColourHSB LineHue (0 ).as(Real )
+ LineSaturation (0 ).as(Real )
+ LineBrightness (0 ).as(Real ) ] :Optional :Contour Color Mode: HSB
+ [-LineColourHSBGradientLineHueFirst (0 ).as(Real )
+ LineSaturationFirst (0 ).as(Real )
+ LineBrightnessFirst (0 ).as(Real )
+ LineHueLast (0 ).as(Real )
+ LineSaturationLast (0 ).as(Real )
+ LineBrightnessLast (0 ).as(Real ) ] :Optional :Contour Color GradientMode: HSB
+ [-LineChange LineColorChange (0.1 ).as(Real ) ] :Optional :Contour Color Change
+ [-LineWidthStart LineWidthStart (0.1 ).as(Real ) ] :Optional :Contour Line Width Step
+ [-LineWidthStep LineWidthStep (0.05 ).as(Real ) ] :Optional :Contour Line Width Step
+ [-ReverseOrder ] :Optional :Reverse Print Order
+ [-Untwist untwist (0.0 ).as(Real ) ] :Optional :Untwist Angle [degree/A], example: (-13,28) = 0.4709576
+ [-UpsideDown ] :Optional :Upside Down
+ [-Centre ] :Optional :Image Centre is at the centre of paper.
+ [-CircleRadius CircleRadius (0.5 ).as(Real ) ] :Optional :Radius of circles in the case of imageCircles
+ [-m[ode] mode (49 ).as(Integer ) ] :Optional :Mode
----- mode -----
1: ImageDensity
2: Contour(DiffrentLineWidth)
<PRE>
Usage: mrcImagePrint3D
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-eye[Position] eyeX (100.0 )eyeY (0.0 )eyeZ (0.0 )] :Optional :Eye Position
- [-plane[Position] planeX (0.0 )planeY (0.0 )planeZ (0.0 )] :Optional :Plane Position
- [-C[ontour] contourLevel (0.0 )... ] :Variable :Contour Level ...
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-stereo Stereo (6.0 ).as(Real ) ] :Optional :Stereo View [degree] around z-axis
+ [-rotation nRotation (60 ).as(Integer )
+ RotationAngle (6.0 ).as(Real ) ] :Optional :(Number, angle) : Rotation View around z-axis
+ [-eye[Position] eyeX (100.0 ).as(Real )
+ eyeY (0.0 ).as(Real )
+ eyeZ (0.0 ).as(Real ) ] :Optional :Eye Position
+ [-plane[Position] planeX (0.0 ).as(Real )
+ planeY (0.0 ).as(Real )
+ planeZ (0.0 ).as(Real ) ] :Optional :Plane Position
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-C[ontour] contourLevel (0.0 ).as(Real ) ... ] :Variable :Contour Level ...
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageProjection
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Mode -----
0: x-y sufacae along z-axis [3D to 2D]
1: y-z sufacae along x-axis [3D to 2D]
-2: x-z sufacae along y-axis [3D to 2D]
-3: x-y sufacae to y-axis [2D/3D to 1D]
-4: x-y sufacae to x-axis [2D/3D to 1D]
+2: z-x sufacae along y-axis [3D to 2D]
+3: z-x sufacae to y-axis [2D/3D to 1D]
+4: y-z sufacae to x-axis [2D/3D to 1D]
5: x-y sufacae to z-axis [2D/3D to 1D]
</PRE>
</BODY>
<PRE>
Usage: mrcImageROI3D
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-x x1 (0.0 )x2 (0.0 )] :Optional :from x1[pixel] to x2[pixel]
- [-y y1 (0.0 )y2 (0.0 )] :Optional :from y1[pixel] to y2[pixel]
- [-z z1 (0.0 )z2 (0.0 )] :Optional :from z1[pixel] to z2[pixel]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-x x1 (0.0 ).as(Real )
+ x2 (0.0 ).as(Real ) ] :Optional :from x1[pixel] to x2[pixel]
+ [-y y1 (0.0 ).as(Real )
+ y2 (0.0 ).as(Real ) ] :Optional :from y1[pixel] to y2[pixel]
+ [-z z1 (0.0 ).as(Real )
+ z2 (0.0 ).as(Real ) ] :Optional :from z1[pixel] to z2[pixel]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
from z1 to z2
</PRE>
<PRE>
Usage: mrcImageROIs
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-I[nformation] Info (NULL )] :Essential :Information
- [-o[utput] Out (NULL )] :Optional :MontageFile
- [-S[hrink] Shrink (NULL )] :Optional :When inputimage was shrunk
- [-width Width (0.0 )] :Optional :Width
- [-height Height (0.0 )] :Optional :Height
- [-NonPeriodic ] :Optional :Zero Outof Range
- [-M[ode] Mode (2 )] :Optional :ImageType:0 byte 1 short 2 float
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-I[nformation] Info (NULL ).as(inFile ) ] :Essential :Information
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :MontageFile
+ [-S[hrink] Shrink (NULL ).as(Integer ) ] :Optional :When inputimage was shrunk
+ [-width Width (0.0 ).as(Real ) ] :Optional :Width
+ [-height Height (0.0 ).as(Real ) ] :Optional :Height
+ [-NonPeriodic ] :Optional :Zero Outof Range
+ [-M[ode] Mode (2 ).as(Integer ) ] :Optional :ImageType:0 byte 1 short 2 float
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- Mode -----
0: Nearest
<PRE>
Usage: mrcImageROItoPCAoutputImage
Options:
- [-i[nput] InList (NULL )] :Essential :Input: filelist
- [-o[utput] OutList (NULL )] :Essential :Output: filelist
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] InList (NULL ).as(inFileListNoOpen ) ] :Essential :Input: filelist
+ [-o[utput] OutList (NULL ).as(outFileListNoOpen ) ] :Essential :Output: filelist
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageRadialDistribution
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (stdout )] :Optional :Output: ASCII
- [-O[utputMRC] Out2 (NULL )] :Optional :Output: MRC
- [-centre Cx (0.0 )Cy (0.0 )] :Optional :[pixel]
- [-Avg ] :Optional :flagAvg: Averaged Intensity
- [-Inv ] :Optional :flagInv: Inversed Intensity
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: ASCII
+ [-O[utputMRC] Out2 (NULL ).as(outFile ) ] :Optional :Output: MRC
+ [-centre Cx (0.0 ).as(Real )
+ Cy (0.0 ).as(Real ) ] :Optional :[pixel]
+ [-Avg ] :Optional :flagAvg: Averaged Intensity
+ [-Inv ] :Optional :flagInv: Inversed Intensity
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageRadonTransform
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-dtheta dtheta (1.0 )] :Optional :Input: detaTheta
- [-dphi dphi (1.0 )] :Optional :Input: detaPhi
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-dtheta dtheta (1.0 ).as(Real ) ] :Optional :Input: detaTheta
+ [-dphi dphi (1.0 ).as(Real ) ] :Optional :Input: detaPhi
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageRandomParticlesImageCreate
Options:
- [-i[nput] In (stdin )] :Essential :Input: ParticlesList[mrcImage]
- [-o[utput] Out (stdout )] :Essential :Output: Image[mrcImage]
- [-N Nx (1024 )Ny (1024 )] :Optional :Input: ImageSize
- [-seed Seed (0 )] :Optional :Input: Seed[]
- [-InterpolationMode InterpolationMode (2 )] :Optional :Input: InterpolationMode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (stdin ).as(inFileList ) ] :Essential :Input: ParticlesList[mrcImage]
+ [-o[utput] Out (stdout ).as(outFile ) ] :Essential :Output: Image[mrcImage]
+ [-N Nx (1024 ).as(Integer )
+ Ny (1024 ).as(Integer ) ] :Optional :Input: ImageSize
+ [-seed Seed (0 ).as(Integer ) ] :Optional :Input: Seed[]
+ [-InterpolationMode InterpolationMode (2 ).as(Integer ) ] :Optional :Input: InterpolationMode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageRealValueAdd
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-v[alue] Value (0 )] :Essential :Input: Value
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-v[alue] Value (0 ).as(Real ) ] :Essential :Input: Value
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageRectangleGet
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-r[oi] blx (0 )bly (0 )trx (0 )try (0 )] :Optional :Rectangle ROI
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-r[oi] blx (0 ).as(Integer )
+ bly (0 ).as(Integer )
+ trx (0 ).as(Integer )
+ try (0 ).as(Integer ) ] :Optional :Rectangle ROI
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageRectangleGetByCorrelation
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-r[eference] Ref (NULL )] :Optional :ReferenceFile
- [-Nx[Number of x] Nx (0 )] :Optional :Nx:Default If Nx of inputfile is even Nx ,else Nx-1
- [-Ny[Number of y] Ny (0 )] :Optional :Ny:Default If Ny of inputfile is even Ny ,else Ny-1
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-r[eference] Ref (NULL ).as(inFile ) ] :Optional :ReferenceFile
+ [-Nx[Number of x] Nx (0 ).as(Integer ) ] :Optional :Nx:Default If Nx of inputfile is even Nx ,else Nx-1
+ [-Ny[Number of y] Ny (0 ).as(Integer ) ] :Optional :Ny:Default If Ny of inputfile is even Ny ,else Ny-1
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageRefConv2D
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode(For fourier space) 0:Absolute Value 1:Phase
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode(For fourier space) 0:Absolute Value 1:Phase
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageRefCreate
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-p[osition] iP (0 )iW (0 )iA (0 )] :Optional :Position of Center of model creation. Phi(degree) ,Omega(degree) ,Alpha(degree)
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-p[osition] iP (0 ).as(Real )
+ iW (0 ).as(Real )
+ iA (0 ).as(Real ) ] :Optional :Position of Center of model creation. Phi(degree) ,Omega(degree) ,Alpha(degree)
:Omega and Alpha range must be around 0 or 180.
- [-w[idth] Wp (360 )Ww (10 )Wa (10 )] :Optional :Width of Phi(degree,plus minus) ,Omega(degree,plus minus) ,Alpha(degree,plus minus)
- [-d[elta] Dp (5 )Dw (5 )Da (5 )] :Optional :Interval of model creation(degree) Phi(around Z axis),Omega(Y axis),Alpha(X axis)
- [-x Wx (NULL )] :Optional :Data length of x in the outputfile.Default:Data length of x in the inputfile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-w[idth] Wp (360 ).as(Real )
+ Ww (10 ).as(Real )
+ Wa (10 ).as(Real ) ] :Optional :Width of Phi(degree,plus minus) ,Omega(degree,plus minus) ,Alpha(degree,plus minus)
+ [-d[elta] Dp (5 ).as(Real )
+ Dw (5 ).as(Real )
+ Da (5 ).as(Real ) ] :Optional :Interval of model creation(degree) Phi(around Z axis),Omega(Y axis),Alpha(X axis)
+ [-x Wx (NULL ).as(Integer ) ] :Optional :Data length of x in the outputfile.Default:Data length of x in the inputfile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageRefFFTConv2D
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageRefScaleChangeWithPad
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Optional :OutputDataFile
- [-r[eference] Ref (NULL )] :Optional :ReferenceDataFile
- [-width width (140 )] :Optional :width [Pixel]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-r[eference] Ref (NULL ).as(inFile ) ] :Optional :ReferenceDataFile
+ [-width width (140 ).as(Real ) ] :Optional :width [Pixel]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageResolutionEstimateForFilaments
Options:
- [-i1[input1] In1 (NULL )] :Optional :InputDataFile
- [-i2[input2] In2 (NULL )] :Optional :InputDataFile
- [-d[elta] delta (0 )] :Optional :Interval of output data(1/A). Default 1/(Nx*size of pixel)
- [-H[ighThreshold] H (0 )] :Optional :High threshold.
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-M[ode2] mode2 (0 )] :Optional :Mode
+ [-i1[input1] In1 (NULL ).as(inFile ) ] :Optional :InputDataFile
+ [-i2[input2] In2 (NULL ).as(inFile ) ] :Optional :InputDataFile
+ [-d[elta] delta (0 ).as(Real ) ] :Optional :Interval of output data(1/A). Default 1/(Nx*size of pixel)
+ [-H[ighThreshold] H (0 ).as(Real ) ] :Optional :High threshold.
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-M[ode2] mode2 (0 ).as(Integer ) ] :Optional :Mode
----- mode -----
0: Fourier shell correlation.
1: Fourier shell phase residual.
<PRE>
Usage: mrcImageReverse
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
y values keep the same.
</PRE>
</BODY>
<PRE>
Usage: mrcImageRotation
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-a[ngle] Angle (90.0 )] :Optional :Angle[degree]
- [-Periodic ] :Optional :Periodic
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode: HowToGet
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-a[ngle] Angle (90.0 ).as(Real ) ] :Optional :Angle[degree]
+ [-Periodic ] :Optional :Periodic
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode: HowToGet
----- Mode -----
0:Nearest
1:Bi-linear Interpolation
<PRE>
Usage: mrcImageRotation3D
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrc
- [-o[utput] Out (NULL )] :Essential :Output: mrc
- [-E[uler]A[ngle] EulerAngle (YOYS )Rot1 (0.0 )Rot2 (0.0 )Rot3 (0.0 )] :Optional :Input: Euler Angle
- [-M[ode] Mode (2 )] :Optional :InterpolationMode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrc
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: mrc
+ [-E[uler]A[ngle] EulerAngle (YOYS ).as(String )
+ Rot1 (0.0 ).as(Real )
+ Rot2 (0.0 ).as(Real )
+ Rot3 (0.0 ).as(Real ) ] :Optional :Input: Euler Angle
+ [-M[ode] Mode (2 ).as(Integer ) ] :Optional :InterpolationMode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
-m
0: padding 0
<PRE>
Usage: mrcImageSN
Options:
- [-i[nput] In (NULL )] :Essential :InputList
- [-A[verage] Avg (NULL )] :Optional :Output: Average
- [-SN SN (NULL )] :Optional :Output: SN:=Average/SD
- [-t t (NULL )] :Optional :Output: t=:Average/SD/sqrt(n-2)
- [-SE SE (NULL )] :Optional :Output: Standard Error
- [-SD SD (NULL )] :Optional :Output: Standard Deviation
- [-Var Var (NULL )] :Optional :Output: Variance
- [-c[onfigFile] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFileList ) ] :Essential :InputList
+ [-A[verage] Avg (NULL ).as(outFile ) ] :Optional :Output: Average
+ [-SN SN (NULL ).as(outFile ) ] :Optional :Output: SN:=Average/SD
+ [-t t (NULL ).as(outFile ) ] :Optional :Output: t=:Average/SD/sqrt(n-2)
+ [-SE SE (NULL ).as(outFile ) ] :Optional :Output: Standard Error
+ [-SD SD (NULL ).as(outFile ) ] :Optional :Output: Standard Deviation
+ [-Var Var (NULL ).as(outFile ) ] :Optional :Output: Variance
+ [-c[onfigFile] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
--- /dev/null
+/bin/bash: mrcImageSNEstimate: No such file or directory
<PRE>
Usage: mrcImageSamplingUnitChange
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-S[amplingUnit] Sx (0.0 )Sy (0.0 )Sz (0.0 )] :Optional :SamplingUnit[A]
- [-N Nx (0.0 )Ny (0.0 )Nz (0.0 )] :Optional :N[Integer]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-S[amplingUnit] Sx (0.0 ).as(Real )
+ Sy (0.0 ).as(Real )
+ Sz (0.0 ).as(Real ) ] :Optional :SamplingUnit[A]
+ [-N Nx (0.0 ).as(Integer )
+ Ny (0.0 ).as(Integer )
+ Nz (0.0 ).as(Real ) ] :Optional :N[Integer]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
---- Mode ----
0: Nearest
1: Linear
<PRE>
Usage: mrcImageScalarAdd
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-x[position] x (0 )] :Optional :x position to add value
- [-y[position] y (0 )] :Optional :y position to add value
- [-z[position] z (0 )] :Optional :z position to add value
- [-v[alue] Value (0.0 )] :Optional :mrcImage + value
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-x[position] x (0 ).as(Real ) ] :Optional :x position to add value
+ [-y[position] y (0 ).as(Real ) ] :Optional :y position to add value
+ [-z[position] z (0 ).as(Real ) ] :Optional :z position to add value
+ [-v[alue] Value (0.0 ).as(Real ) ] :Optional :mrcImage + value
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
mode 0:Scalar value is added to each pixel.
mode 1:Scalar value is added to one pixel.
<PRE>
Usage: mrcImageSectionGet
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-z z (0 )] :Optional :z-Section number
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFileNoOpen ) ] :Essential :OutputDataFile
+ [-z z (0 ).as(Integer ) ] :Optional :z-Section number: -1 Serial section
+ [-e[xtention] format (%s.%04d ).as(String ) ] :Optional :Serial section format
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
mode 0: Copy the selected section into a new area indicated by dst
mode 1: Share the selected section between dst and src: replacement of pointers
<PRE>
Usage: mrcImageSetFunction
Options:
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageShapeOrientation
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrcImage
- [-o[utput] Out (stdout )] :Optional :Output: ASCII
- [-thres[hold] threshold (0 )] :Optional :Threshold: if dens<thres, pixel is ignored.
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrcImage
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: ASCII
+ [-thres[hold] threshold (0 ).as(Real ) ] :Optional :Threshold: if dens<thres, pixel is ignored.
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
[-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input: mrcImage
[-o[utput] Out (stdout ).as(outFile::ASCII ) ] :Optional :Output: ASCII
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-m[ode] mode (1 ).as(Integer ) ] :Optional :Mode
[-C[ontour] Contour (1.0 ).as(Real ) ... ] :Variable :Contour
----- Additional Usage -----
-C : ContourLevels
100% 60% 40%
----- Objectives -----
Determine the orientations/molecular axis by PCA alogrism
- $ mrcImagePCA -i mrc -o parameter -C C1 C2 C3 ...
+ $ mrcImageShapePCA -i mrc -o parameter -C C1 C2 C3 ...
+-m
+ +1: Sphere (default)
+ +2: Disk
+ +4: Cylinder
</PRE>
</BODY>
<PRE>
Usage: mrcImageShapePCAFit
Options:
- [-i[nput] In (NULL )] :Essential :Input: test(mrcImage)
- [-r[eference] Ref (NULL )] :Essential :Input: ref(mrcImage)
- [-o[utput] Out (stdout )] :Optional :Output: Parameters
- [-fit Fit (NULL )] :Optional :Output: fit(mrcImage) <- test
- [-fitMat FitMat (NULL )] :Optional :Output: Matrix3D for fit(mrcImage) <- test
- [-iMode IMode (2 )] :Optional :InterpolationMode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-C[ontour] Contour (1.0 )... ] :Variable :Contour(test/ref)
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: test(mrcImage)
+ [-r[eference] Ref (NULL ).as(inFile ) ] :Essential :Input: ref(mrcImage)
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: Parameters
+ [-fit Fit (NULL ).as(outFile ) ] :Optional :Output: fit(mrcImage) <- test
+ [-fitMat FitMat (NULL ).as(outFile ) ] :Optional :Output: Matrix3D for fit(mrcImage) <- test
+ [-iMode IMode (2 ).as(Integer ) ] :Optional :InterpolationMode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-C[ontour] Contour (1.0 ).as(Real ) ... ] :Variable :Contour(test/ref)
----- Additional Usage -----
</PRE>
</BODY>
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImageShapeSearch</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageShapeSearch</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageShapeSearch
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output
+ [-Shape Shape (NULL ).as(outFile::mrcImage ) ] :Optional :Output
+ [-n[Cube] nCube (0 ).as(Integer ) ] :Optional :Mode
+ [-r[adius] minR (3 ).as(Integer )
+ maxR (5 ).as(Integer )
+ delR (1 ).as(Integer ) ] :Optional :Radius[pixel]
+ [-l[ength] minL (3 ).as(Integer )
+ maxL (5 ).as(Integer )
+ delL (1 ).as(Integer ) ] :Optional :Length[pixel]
+ [-O[utput]V[ector]BILDOutVectorBILD (NULL ).as(outFile::BILD ) ] :Optional :Output:BILD-vector
+ [-Phi minPhi (0.0 ).as(Real )
+ maxPhi (359.0 ).as(Real )
+ delPhi (45.0 ).as(Real ) ] :Optional :around z-axis[degree]
+ [-Theta minTheta (0.0 ).as(Real )
+ maxTheta (359.0 ).as(Real )
+ delTheta (45.0 ).as(Real ) ] :Optional :around x-axis[degree]
+ [-Psi minPsi (0.0 ).as(Real )
+ maxPsi (350.0 ).as(Real )
+ delPsi (45.0 ).as(Real ) ] :Optional :around x-axis[degree]
+ [-thres[Zscore] thresZscore (1.0 ).as(Real ) ] :Optional :Zscore
+ [-interp[olationMode]interpMode (0 ).as(Integer ) ] :Optional :interpMode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+0: Cylinder with radius and length
+1: Disk with radius and length(thickness)
+2: Sphere with radius
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: mrcImageShift
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-x[shift] xshift (0.0 )] :Optional :x-shift[pixel]
- [-y[shift] yshift (0.0 )] :Optional :y-shift[pixel]
- [-z[shift] zshift (0.0 )] :Optional :z-shift[pixel]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-x[shift] xshift (0.0 ).as(Real ) ] :Optional :x-shift[pixel]
+ [-y[shift] yshift (0.0 ).as(Real ) ] :Optional :y-shift[pixel]
+ [-z[shift] zshift (0.0 ).as(Real ) ] :Optional :z-shift[pixel]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageShiftFollowingGC
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-I[nverse] ] :Optional :DensityInverse
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-I[nverse] ] :Optional :DensityInverse
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageShrink
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-S[hrink] S (2 )] :Optional :Shrink(1/S)
- [-S[hrink]x Sx (2 )] :Optional :Shrink(1/S) for x axis.
- [-S[hrink]y Sy (2 )] :Optional :Shrink(1/S) for y axis.
- [-S[hrink]z Sz (2 )] :Optional :Shrink(1/S) for z axis.
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-S[hrink] S (2 ).as(Integer ) ] :Optional :Shrink(1/S)
+ [-S[hrink]x Sx (2 ).as(Integer ) ] :Optional :Shrink(1/S) for x axis.
+ [-S[hrink]y Sy (2 ).as(Integer ) ] :Optional :Shrink(1/S) for y axis.
+ [-S[hrink]z Sz (2 ).as(Integer ) ] :Optional :Shrink(1/S) for z axis.
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
---- Note -----
If S = 2, N.x -> N.x/2 and Length.x -> 2*Length.x.
Image 0 0 1 1 -> Image 0 1
<PRE>
Usage: mrcImageSimilarImageSearch
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFileList ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageSimilarityEstimate
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] information fileOut (NULL )] :Optional :OutputDataFile
- [-o[utput] Cor[relation]OutCor (NULL )] :Optional :OutputDataFile
- [-ref[erence array of file]ref (stdin )] :Essential :InputDataFiles
- [-cor[relation] file namecorfilename (stdin )] :Optional :InputDataFiles
- [-cormode cormode (0 )] :Optional :Mode
- [-ctfinfo ctfinfo (NULL )] :Optional :InputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] information fileOut (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-o[utput] Cor[relation]OutCor (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-ref[erence array of file]ref (stdin ).as(inFileListNoOpen ) ] :Essential :InputDataFiles
+ [-cor[relation] file namecorfilename (stdin ).as(inFileListNoOpen ) ] :Optional :InputDataFiles
+ [-cormode cormode (0 ).as(Integer ) ] :Optional :Mode
+ [-ctfinfo ctfinfo (NULL ).as(inFile ) ] :Optional :InputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
cormode:(lmrcImageCorrelation)
0: Normal Correlation FxG*
<PRE>
Usage: mrcImageSinogramCorrelation
Options:
- [-i[nput] In (NULL )] :Essential :Input: in[sinogram: mrc]
- [-r[ef] Ref (NULL )] :Essential :Input: ref[sinogram: mrc]
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-w[eigth] w0th (1.0 )w1st (0.0 )w2nd (0.0 )] :Optional :Weigth for Mode: 1
- [-T[hreshold] threshold (0.0 )] :Optional :threshold for Mode: 2
- [-M[odeforCorrelation]corMode (0 )] :Optional :Mode: for Correlation
- [-L[ength]M[ode] LengthMode (0 )] :Optional :Length Mode: for LengthCorrelation
- [-L[ength]T[hreshold]M[ode]LengthThresholdMode (0 )] :Optional :Length Threshold Mode: for LengthCorrelation
- [-L[ength]T[hreshold]R[atio]LengthThresholdRatio(1.0 )] :Optional :ratio of threshold for LenthMode: 1
- [-L[ength]C[orrelation]M[ode]LCMode (0 )] :Optional :Mode: for LengthCorrelationMode
- [-L[ength]C[orrelation]T[hreshold]LengthCorrelationThreshold(0.0 )] :Optional :threshold for LengthCorrelation
- [-w[eight]L[ength] weightLength (1.0 )] :Optional :Weight for LengthCorrelation
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: in[sinogram: mrc]
+ [-r[ef] Ref (NULL ).as(inFile ) ] :Essential :Input: ref[sinogram: mrc]
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-w[eigth] w0th (1.0 ).as(Real )
+ w1st (0.0 ).as(Real )
+ w2nd (0.0 ).as(Real ) ] :Optional :Weigth for Mode: 1
+ [-T[hreshold] threshold (0.0 ).as(Real ) ] :Optional :threshold for Mode: 2
+ [-M[odeforCorrelation]corMode (0 ).as(Integer ) ] :Optional :Mode: for Correlation
+ [-L[ength]M[ode] LengthMode (0 ).as(Integer ) ] :Optional :Length Mode: for LengthCorrelation
+ [-L[ength]T[hreshold]M[ode]LengthThresholdMode (0 ).as(Integer ) ] :Optional :Length Threshold Mode: for LengthCorrelation
+ [-L[ength]T[hreshold]R[atio]LengthThresholdRatio(1.0 ).as(Real ) ] :Optional :ratio of threshold for LenthMode: 1
+ [-L[ength]C[orrelation]M[ode]LCMode (0 ).as(Integer ) ] :Optional :Mode: for LengthCorrelationMode
+ [-L[ength]C[orrelation]T[hreshold]LengthCorrelationThreshold(0.0 ).as(Real ) ] :Optional :threshold for LengthCorrelation
+ [-w[eight]L[ength] weightLength (1.0 ).as(Real ) ] :Optional :Weight for LengthCorrelation
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- LengthMode -----
-LM = 0 : without Length Correlation
<PRE>
Usage: mrcImageSinogramCreate
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-dphi dphi (1.0 )] :Optional :Input: dphi[degree] in mode=0 and 1
- [-S[mall]dphi Smalldphi (1.0 )] :Optional :Input: Smalldphi[degree] in mode=1
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-dphi dphi (1.0 ).as(Real ) ] :Optional :Input: dphi[degree] in mode=0 and 1
+ [-S[mall]dphi Smalldphi (1.0 ).as(Real ) ] :Optional :Input: Smalldphi[degree] in mode=1
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageSinogramFFT
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageSmoothing
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-sx sx (3 )] :Optional :x of Kernel Size
- [-sy sy (3 )] :Optional :y of Kernel Size
- [-sz sz (3 )] :Optional :z of Kernel Size
- [-r r (1 )] :Optional :Radius of Kernel Size
- [-sigma sigma (2.0 )] :Optional :Sigma for Lee-Sigma
- [-times times (1 )] :Optional :Repeat time
- [-m[ode] mode (0 )] :Optional :Mode
- [-M[ode2] mode2 (0 )] :Optional :Mode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-sx sx (3 ).as(Real ) ] :Optional :x of Kernel Size
+ [-sy sy (3 ).as(Real ) ] :Optional :y of Kernel Size
+ [-sz sz (3 ).as(Real ) ] :Optional :z of Kernel Size
+ [-r r (1 ).as(Real ) ] :Optional :Radius of Kernel Size
+ [-sigma sigma (2.0 ).as(Real ) ] :Optional :Sigma for Lee-Sigma
+ [-times times (1 ).as(Integer ) ] :Optional :Repeat time
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-M[ode2] mode2 (0 ).as(Integer ) ] :Optional :Mode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
>>> Mode <<<<
1: Median filter
2: Mean filter
<PRE>
Usage: mrcImageSolventFlattening
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-rmax rmax (190 )] :Optional :rmax [A]
- [-sd Range (0 )] :Optional :Assign voxels below MeanOfSolvent+Range*SDofSolvent as Solvent
- [-density density (0 )] :Optional :embed mean lower than density value
- [-Floating ] :Optional :data minus mean of Solvent
- [-oparam[eter] OutParam (stdout )] :Optional :Output: Parameters
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-rmax rmax (190 ).as(Real ) ] :Optional :rmax [A]
+ [-sd Range (0 ).as(Real ) ] :Optional :Assign voxels below MeanOfSolvent+Range*SDofSolvent as Solvent
+ [-density density (0 ).as(Real ) ] :Optional :embed mean lower than density value
+ [-Floating ] :Optional :data minus mean of Solvent
+ [-oparam[eter] OutParam (stdout ).as(outFile ) ] :Optional :Output: Parameters
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
-m 0: mean of all density
1: mean of sphere surface density at rmax
[-filter filterIn (NULL ).as(inFile::ASCII ) ] :Essential :Input: filterFile
[-filterCol[lumn] colR (1 ).as(Integer )
colW (2 ).as(Integer ) ] :Optional :R W
- [-o[utput] Out (NULL ).as(outFile::ASCII ) ] :Essential :Output: mrcImage
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output: mrcImage
[-L[owCut] Low (-0.1 ).as(Real ) ] :Optional :LowCut: [/A]
[-H[ighCut] High (1.0 ).as(Real ) ] :Optional :HighCut: [/A]
[-c[onfig] configFile (NULL ).as(inFile::ASCII ) ] :Optional :ConfigurationFile
<PRE>
Usage: mrcImageSphere
Options:
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-size size (5 )] :Optional :Pixel Size[A]
- [-r[adius] r (5 )] :Optional :radius[Pixel]
- [-w[eight] w (100 )] :Optional :Weight
- [-m[ode] mode (0 )] :Optional :Mode
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-size size (5 ).as(Real ) ] :Optional :Pixel Size[A]
+ [-r[adius] r (5 ).as(Real ) ] :Optional :radius[Pixel]
+ [-w[eight] w (100 ).as(Real ) ] :Optional :Weight
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
mode 0 char
mode 2 float
<PRE>
Usage: mrcImageSplit
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrcImage
- [-o[utput] Out ( )] :Optional :Output: Basename
- [-s[uffix] Suffix (205625115200000064.splt)] :Optional :Output: Suffix
- [-H[eight] Height (0 )] :Optional :Input: Height[y]: SplitSize [pixel]
- [-W[idth] Width (0 )] :Optional :Input: Width[x]: SplitSize [pixel]
- [-S[ection] Section (0 )] :Optional :Input: Section[z]: SplitSize [pixel]
- [-H[eight]A[ngstrom] HeightA (0 )] :Optional :Input: Height: SplitSize [A]
- [-W[idth]A[ngstrom] WidthA (0 )] :Optional :Input: Width: SplitSize [A]
- [-S[ection]A[ngstrom]SectionA (0 )] :Optional :Input: Section: SplitSize [A]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrcImage
+ [-o[utput] Out ( ).as(String ) ] :Optional :Output: Basename
+ [-s[uffix] Suffix (%04d%04d%04d.splt).as(String ) ] :Optional :Output: Suffix
+ [-H[eight] Height (0 ).as(Integer ) ] :Optional :Input: Height[y]: SplitSize [pixel]
+ [-W[idth] Width (0 ).as(Integer ) ] :Optional :Input: Width[x]: SplitSize [pixel]
+ [-S[ection] Section (0 ).as(Integer ) ] :Optional :Input: Section[z]: SplitSize [pixel]
+ [-H[eight]A[ngstrom] HeightA (0 ).as(Integer ) ] :Optional :Input: Height: SplitSize [A]
+ [-W[idth]A[ngstrom] WidthA (0 ).as(Integer ) ] :Optional :Input: Width: SplitSize [A]
+ [-S[ection]A[ngstrom]SectionA (0 ).as(Integer ) ] :Optional :Input: Section: SplitSize [A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageSquare
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-eps eps (1e-15 )] :Optional :Epsilon to consider zero. For mode 1 only
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-eps eps (1e-15 ).as(Real ) ] :Optional :Epsilon to consider zero. For mode 1 only
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
mode 0: Square
mode 1: Square Root
<PRE>
Usage: mrcImageStandardDeviation
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-h[ighThreshold] Hth (0 )] :Optional :High threshold. Mode2=0 only.
- [-l[ow threshold] Lth (0 )] :Optional :Low threshold. Mode2=0 only.
- [-m[ode] mode (0 )] :Optional :Mode
- [-M[ode2] mode2 (0 )] :Optional :Mode2
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-h[ighThreshold] Hth (0 ).as(Real ) ] :Optional :High threshold. Mode2=0 only.
+ [-l[ow threshold] Lth (0 ).as(Real ) ] :Optional :Low threshold. Mode2=0 only.
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-M[ode2] mode2 (0 ).as(Integer ) ] :Optional :Mode2
----- Additional Usage -----
Input file is a list of mrc files.
mode 0: Standard deviation
<PRE>
Usage: mrcImageSubtraction
Options:
- [-i1[input1] In1 (NULL )] :Essential :InputDataFile1
- [-i2[input2] In2 (NULL )] :Essential :InputDataFile2
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-rmsd RMSD (stdout )] :Optional :Output:
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i1[input1] In1 (NULL ).as(inFile ) ] :Essential :InputDataFile1
+ [-i2[input2] In2 (NULL ).as(inFile ) ] :Essential :InputDataFile2
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-rmsd RMSD (stdout ).as(outFile ) ] :Optional :Output:
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
mode 0:out = in1 - in2
1:out = abs (in1 - in2)
<PRE>
Usage: mrcImageSuperResolution
Options:
- [-I[nput] InOriginal (NULL )] :Essential :Input: Original
- [-i[nput] InPrevious (NULL )] :Essential :Input: Previous
- [-i[nput]c[ounter] FFTInCount (NULL )] :Optional :Input: CounterforWeight FourierSpace
- [-o[utput] Out (NULL )] :Essential :Output: Next
- [-t[ime] t (1 )] :Optional :Number of time: Iteration(Real Space)
- [-fromp[oint]1 x00 (0 )y00 (0 )z00 (0 )] :Optional :First value near origin of coordinates: x00[pixel] y00[pixel] z00[pixel]
- [-top[oint]1 x01 (2 )y01 (2 )z01 (2 )] :Optional :target value: x01[pixel] y01[pixel] z01[pixel]
- [-fromp[oint]2 x10 (0 )y10 (0 )z10 (0 )] :Optional :First value far from origin of coordinates: x10[pixel] y10[pixel] z10[pixel]
- [-top[oint]2 x11 (0 )y11 (0 )z11 (0 )] :Optional :target value: x11[pixel] y11[pixel] z11[pixel]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Essential :RealSpaceCalculating
- [-LabelingMode labelingmode (0 )] :Optional :LabelingMode
- [-max[value] max (800 )] :Optional :Density Max value:Support Constraint()
- [-min[value] min (200 )] :Optional :Density Min value:Support Constraint()
- [-sh[ape] shape (0 )] :Optional :Shape:0(Rectangule),1(Globe)
- [-h[alf]v[alue]p[oint]hvp (0.0 )] :Optional :Half value point(/[A])
- [-Inverse ] :Optional :Inverse
- [-nM[olecule] nMolecule (1 )] :Optional :Number of Molecule
- [-M[olecularWeight] MolecularWeight (80000 )] :Optional :MolecularWeight
- [-D[ensity] Density (1.35 )] :Optional :Density(g/cm3)
- [-counter incounter (3.0 )] :Optional :Counter(Fourier Space)
- [-d[elta]Density deltaDens (100.0 )] :Optional :Delta (Convergence)
- [-d[elta]Area deltaArea (100.0 )] :Optional :Area (Convergence)
- [-sub[traction] sub (0.2 )] :Optional :Subtraction(Convergence)
- [-ratio ratio (0.3 )] :Optional :Ratio(Convergence)
- [-t[ime]max tmax (1000 )] :Optional :Time Max(Convergence)
- [-w[eight]d[elta] WeightDelta (0.1 )] :Optional :WeightDelta(Fourier Space)
- [-w[eight]m[ax] WeightMax (2 )] :Optional :WeightMax(Fourier Space)
- [-Subtraction ] :Optional :Subtraction(Real Space)
+ [-I[nput] InOriginal (NULL ).as(inFile ) ] :Essential :Input: Original
+ [-i[nput] InPrevious (NULL ).as(inFile ) ] :Essential :Input: Previous
+ [-i[nput]c[ounter] FFTInCount (NULL ).as(inFile ) ] :Optional :Input: CounterforWeight FourierSpace
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: Next
+ [-t[ime] t (1 ).as(Integer ) ] :Optional :Number of time: Iteration(Real Space)
+ [-fromp[oint]1 x00 (0 ).as(Integer )
+ y00 (0 ).as(Integer )
+ z00 (0 ).as(Integer ) ] :Optional :First value near origin of coordinates: x00[pixel] y00[pixel] z00[pixel]
+ [-top[oint]1 x01 (2 ).as(Integer )
+ y01 (2 ).as(Integer )
+ z01 (2 ).as(Integer ) ] :Optional :target value: x01[pixel] y01[pixel] z01[pixel]
+ [-fromp[oint]2 x10 (0 ).as(Integer )
+ y10 (0 ).as(Integer )
+ z10 (0 ).as(Integer ) ] :Optional :First value far from origin of coordinates: x10[pixel] y10[pixel] z10[pixel]
+ [-top[oint]2 x11 (0 ).as(Integer )
+ y11 (0 ).as(Integer )
+ z11 (0 ).as(Integer ) ] :Optional :target value: x11[pixel] y11[pixel] z11[pixel]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Essential :RealSpaceCalculating
+ [-LabelingMode labelingmode (0 ).as(Integer ) ] :Optional :LabelingMode
+ [-max[value] max (800 ).as(Integer ) ] :Optional :Density Max value:Support Constraint()
+ [-min[value] min (200 ).as(Integer ) ] :Optional :Density Min value:Support Constraint()
+ [-sh[ape] shape (0 ).as(Integer ) ] :Optional :Shape:0(Rectangule),1(Globe)
+ [-h[alf]v[alue]p[oint]hvp (0.0 ).as(Real ) ] :Optional :Half value point(/[A])
+ [-Inverse ] :Optional :Inverse
+ [-nM[olecule] nMolecule (1 ).as(Integer ) ] :Optional :Number of Molecule
+ [-M[olecularWeight] MolecularWeight (80000 ).as(Integer ) ] :Optional :MolecularWeight
+ [-D[ensity] Density (1.35 ).as(Real ) ] :Optional :Density(g/cm3)
+ [-counter incounter (3.0 ).as(Real ) ] :Optional :Counter(Fourier Space)
+ [-d[elta]Density deltaDens (100.0 ).as(Real ) ] :Optional :Delta (Convergence)
+ [-d[elta]Area deltaArea (100.0 ).as(Real ) ] :Optional :Area (Convergence)
+ [-sub[traction] sub (0.2 ).as(Real ) ] :Optional :Subtraction(Convergence)
+ [-ratio ratio (0.3 ).as(Real ) ] :Optional :Ratio(Convergence)
+ [-t[ime]max tmax (1000 ).as(Integer ) ] :Optional :Time Max(Convergence)
+ [-w[eight]d[elta] WeightDelta (0.1 ).as(Real ) ] :Optional :WeightDelta(Fourier Space)
+ [-w[eight]m[ax] WeightMax (2 ).as(Integer ) ] :Optional :WeightMax(Fourier Space)
+ [-Subtraction ] :Optional :Subtraction(Real Space)
----- Additional Usage -----
-m Option
1 : AreaAndLocation
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImageSurfaceAreaCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageSurfaceAreaCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageSurfaceAreaCalc
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :OutputDataFile
+ [-o[utput]S[urface] OutSurface (NULL ).as(outFile::mrcImage ) ] :Optional :Output:Surface
+ [-o[utput]S[urface]A[rea]OutSurfaceArea (stdout ).as(outFile::ASCII ) ] :Optional :Output:Surface
+ [-n[eighbor] Neighbor (0 ).as(Integer ) ] :Optional :Neighbor: 6(0)|18|26
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImageSurfaceCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageSurfaceCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageSurfaceCalc
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-n[eighbor] neighbor (26 ).as(Integer ) ] :Optional :Neighbor[6|18|26]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: mrcImageSymmetryAverage
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-n[sym] NSym (8 )] :Optional :nsym
- [-centre cx (0 )cy (0 )cz (0 )] :Optional :Centre:
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-n[sym] NSym (8 ).as(Real ) ] :Optional :nsym
+ [-centre cx (0 ).as(Real )
+ cy (0 ).as(Real )
+ cz (0 ).as(Real ) ] :Optional :Centre:
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageSymmetryCentreFind
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrcImage
- [-o[utput] Out (NULL )] :Optional :Output: mrcImage
- [-O[utput] Out2 (stdout )] :Optional :Output: ASCII
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrcImage
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :Output: mrcImage
+ [-O[utput] Out2 (stdout ).as(outFile ) ] :Optional :Output: ASCII
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageSymmetryFind
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Optional :Output: correlation
- [-O[utput] Out2 (stdout )] :Optional :Output: SymmetryInformation
- [-A[verage] Avg (NULL )] :Optional :Output: Average
- [-centreMode centreMode (1 )] :Optional :Input: 0 : Gravity of Centre; 1 : Search n-fold
- [-t1[threshold1] threshold1 (1.8 )] :Optional :Threshold of CheckByAdd
- [-t2[threshold2] threshold2 (0.9 )] :Optional :Threshold in deciding the symmetry number
- [-m1[mode1] mode1 (3 )] :Optional :Mode of Check
- [-m2[mode2] mode2 (2 )] :Optional :Mode of Substruction
- [-dr[delta r] dr (1 )] :Optional :Delta r of outputfile.
- [-dtheta[delta theta]dtheta (1 )] :Optional :Delta theta of outputfile.[DEGREE]
- [-n[umber] n (10 )] :Optional :Check to the number.
- [-n[umber]Range nmin (2 )nmax (10 )] :Optional :Check to the number.
- [-In Image (NULL )Back (NULL )] :Optional :InputDataFile: Image and Back
- [-rangex minx (-3 )maxx (3 )delx (1 )] :Optional :Input:
- [-rangey miny (-3 )maxy (3 )dely (1 )] :Optional :Input:
- [-rangez minz (0 )maxz (0 )delz (1 )] :Optional :Input:
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :Output: correlation
+ [-O[utput] Out2 (stdout ).as(outFile ) ] :Optional :Output: SymmetryInformation
+ [-A[verage] Avg (NULL ).as(outFile ) ] :Optional :Output: Average
+ [-centreMode centreMode (1 ).as(Integer ) ] :Optional :Input: 0 : Gravity of Centre; 1 : Search n-fold
+ [-t1[threshold1] threshold1 (1.8 ).as(Real ) ] :Optional :Threshold of CheckByAdd
+ [-t2[threshold2] threshold2 (0.9 ).as(Real ) ] :Optional :Threshold in deciding the symmetry number
+ [-m1[mode1] mode1 (3 ).as(Integer ) ] :Optional :Mode of Check
+ [-m2[mode2] mode2 (2 ).as(Integer ) ] :Optional :Mode of Substruction
+ [-dr[delta r] dr (1 ).as(Real ) ] :Optional :Delta r of outputfile.
+ [-dtheta[delta theta]dtheta (1 ).as(Real ) ] :Optional :Delta theta of outputfile.[DEGREE]
+ [-n[umber] n (10 ).as(Integer ) ] :Optional :Check to the number.
+ [-n[umber]Range nmin (2 ).as(Integer )
+ nmax (10 ).as(Integer ) ] :Optional :Check to the number.
+ [-In Image (NULL ).as(inFileList )
+ Back (NULL ).as(inFileList ) ] :Optional :InputDataFile: Image and Back
+ [-rangex minx (-3 ).as(Real )
+ maxx (3 ).as(Real )
+ delx (1 ).as(Real ) ] :Optional :Input:
+ [-rangey miny (-3 ).as(Real )
+ maxy (3 ).as(Real )
+ dely (1 ).as(Real ) ] :Optional :Input:
+ [-rangez minz (0 ).as(Real )
+ maxz (0 ).as(Real )
+ delz (1 ).as(Real ) ] :Optional :Input:
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
----- Additional Usage -----
>>>> check type mode
1 : Check by Add
<PRE>
Usage: mrcImageTfunction
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-sx sx (25 )] :Optional :x of Kernel Size
- [-sy sy (25 )] :Optional :y of Kernel Size
- [-sz sz (1 )] :Optional :z of Kernel Size
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-sx sx (25 ).as(Integer ) ] :Optional :x of Kernel Size
+ [-sy sy (25 ).as(Integer ) ] :Optional :y of Kernel Size
+ [-sz sz (1 ).as(Integer ) ] :Optional :z of Kernel Size
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageTiltAxisSearch
Options:
- [-i[nput] In (NULL )] :Optional :In: MRC
- [-I[nput] InList (NULL )] :Optional :In: MRC
- [-r[ef] Ref (NULL )] :Essential :Ref: MRC
- [-o[utput] Out (NULL )] :Essential :Output: Correlation
- [-O[utput] Out2 (stdout )] :Optional :Output: Estimated
- [-range thetaMin (-90 )thetaMax (+90 )thetaDelta (1 )] :Optional :Search Range [degree]
- [-w[idth] Width (0.5 )] :Optional :Projection Range[MIn(Nx,Ny)*Width] around centre
- [-M[ode] Mode (2 )] :Optional :Interpolation Mode
- [-C[orrelation]M[ode]CorrelationMode (17 )] :Optional :Correlation Mode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Optional :In: MRC
+ [-I[nput] InList (NULL ).as(inFileList ) ] :Optional :In: MRC
+ [-r[ef] Ref (NULL ).as(inFile ) ] :Essential :Ref: MRC
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: Correlation
+ [-O[utput] Out2 (stdout ).as(outFile ) ] :Optional :Output: Estimated
+ [-range thetaMin (-90 ).as(Real )
+ thetaMax (+90 ).as(Real )
+ thetaDelta (1 ).as(Real ) ] :Optional :Search Range [degree]
+ [-w[idth] Width (0.5 ).as(Real ) ] :Optional :Projection Range[MIn(Nx,Ny)*Width] around centre
+ [-M[ode] Mode (2 ).as(Integer ) ] :Optional :Interpolation Mode
+ [-C[orrelation]M[ode]CorrelationMode (17 ).as(Integer ) ] :Optional :Correlation Mode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageTiltAxisSearchHelp
Options:
- [-I[nput] InList (NULL )] :Essential :Input:ImageFileList
- [-o[utput]1d Out1D (NULL )] :Optional :Output:
- [-o[utput]1de[nlarged]Out1DEnlarged (NULL )] :Optional :Output:
- [-o[utput]2d Out2D (NULL )] :Optional :Output:
- [-a[xis]P[osition] OriginX (0.0 )OriginY (0.0 )OriginZ (0.0 )] :Optional :Input: AxisPosition
- [-a[xisAngle] AxisAngleYaw (0.0 )AxisAnglePitch (0.0 )] :Optional :Input: AxisAngleYaw/Pitch[degree]
- [-R Rmin (0.05 )Rmax (0.1 )] :Optional :Input: LowPathFiltering
- [-Interp[olationMode]InterpolationMode (2 )] :Optional :Input: InterpolationMode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-I[nput] InList (NULL ).as(inFileList ) ] :Essential :Input:ImageFileList
+ [-o[utput]1d Out1D (NULL ).as(outFile ) ] :Optional :Output:
+ [-o[utput]1de[nlarged]Out1DEnlarged (NULL ).as(outFile ) ] :Optional :Output:
+ [-o[utput]2d Out2D (NULL ).as(outFile ) ] :Optional :Output:
+ [-a[xis]P[osition] OriginX (0.0 ).as(Real )
+ OriginY (0.0 ).as(Real )
+ OriginZ (0.0 ).as(Real ) ] :Optional :Input: AxisPosition
+ [-a[xisAngle] AxisAngleYaw (0.0 ).as(Real )
+ AxisAnglePitch (0.0 ).as(Real ) ] :Optional :Input: AxisAngleYaw/Pitch[degree]
+ [-R Rmin (0.05 ).as(Real )
+ Rmax (0.1 ).as(Real ) ] :Optional :Input: LowPathFiltering
+ [-Interp[olationMode]InterpolationMode (2 ).as(Integer ) ] :Optional :Input: InterpolationMode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
-I fileList format
filename tiltAngle[degree] relativeTiltAxisYaw[degree] relativeTiltAxisPitch[degree] relativePosX[pixel] relativePosY[pixel] relativePosZ[pixel]
<PRE>
Usage: mrcImageToNAMDConstantForces
Options:
- [-i[nput] In (NULL )] :Essential :Input:MRC
- [-ip[db] InPDB (NULL )] :Essential :Input:PDB
- [-o[utput] Out (stdout )] :Optional :Output: PDB with Constant Force
- [-w[eight] Weight (1.0 )] :Optional :Input: Weight for Constant Force
- [-s[calingFactor] ScalingFactor (1.0 )] :Optional :Input: Scaling Factor for Constant Force
- [-C[ontour] Contour (0.0 )] :Optional :Input: Contour[if density>Contour, force=0]
- [-R[otatemode] Rotate (0 )] :Optional :Input: RotateMode
- [-RW[eight] RWeight (0.1 )] :Optional :Input: RotateWeight
- [-S[eed] Seed (0.0 )] :Optional :Input: Seed
- [-nowat[er] ] :Optional :No force for WAT (water residue)
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input:MRC
+ [-ip[db] InPDB (NULL ).as(inFile ) ] :Essential :Input:PDB
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: PDB with Constant Force
+ [-w[eight] Weight (1.0 ).as(Real ) ] :Optional :Input: Weight for Constant Force
+ [-s[calingFactor] ScalingFactor (1.0 ).as(Real ) ] :Optional :Input: Scaling Factor for Constant Force
+ [-C[ontour] Contour (0.0 ).as(Real ) ] :Optional :Input: Contour[if density>Contour, force=0]
+ [-R[otatemode] Rotate (0 ).as(Integer ) ] :Optional :Input: RotateMode
+ [-RW[eight] RWeight (0.1 ).as(Real ) ] :Optional :Input: RotateWeight
+ [-S[eed] Seed (0.0 ).as(Real ) ] :Optional :Input: Seed
+ [-nowat[er] ] :Optional :No force for WAT (water residue)
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
More Density is lower potential.
</PRE>
<PRE>
Usage: mrcImageToPointsSet
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrc
- [-o[utput] Out (stdout )] :Optional :Output: Coord Set
- [-t[hreshold] Threshold (0.0 )] :Optional :Input: threshold
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrc
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: Coord Set
+ [-t[hreshold] Threshold (0.0 ).as(Real ) ] :Optional :Input: threshold
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImageToneReversal</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageToneReversal</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageToneReversal
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: mrcImageTrans
Options:
- [-i[nput] In (NULL )] :Essential :Input: mrc3D
- [-o[utput] Out (NULL )] :Essential :Output: mrc3D
- [-M[atrix] InMatrix (NULL )] :Essential :Input: Matrix3D
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrc3D
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: mrc3D
+ [-M[atrix] InMatrix (NULL ).as(inFile ) ] :Essential :Input: Matrix3D
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
mode: Interpolation mode
</PRE>
<PRE>
Usage: mrcImageTransformDescartesIntoPolar
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-dr dr (1 )] :Optional :Delta r of outputfile[A].
- [-dtheta dtheta (1 )] :Optional :Delta theta of outputfile.[degree]
- [-dphi dphi (1 )] :Optional :Delta phi of outputfile.[degree]
- [-zaxis zx (0 )zy (0 )zz (1 )] :Optional :vector of z-axis
- [-xaxis xx (1 )xy (0 )xz (0 )] :Optional :vector of x-axis
- [-centre cx (0 )cy (0 )cz (0 )] :Optional :centre of image
- [-rweight ] :Optional :r-weighted
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-dr dr (1 ).as(Real ) ] :Optional :Delta r of outputfile[A].
+ [-dtheta dtheta (1 ).as(Real ) ] :Optional :Delta theta of outputfile.[degree]
+ [-dphi dphi (1 ).as(Real ) ] :Optional :Delta phi of outputfile.[degree]
+ [-zaxis zx (0 ).as(Real )
+ zy (0 ).as(Real )
+ zz (1 ).as(Real ) ] :Optional :vector of z-axis
+ [-xaxis xx (1 ).as(Real )
+ xy (0 ).as(Real )
+ xz (0 ).as(Real ) ] :Optional :vector of x-axis
+ [-centre cx (0 ).as(Real )
+ cy (0 ).as(Real )
+ cz (0 ).as(Real ) ] :Optional :centre of image
+ [-rweight ] :Optional :r-weighted
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
>>>>> -m
0 : Image centre is gravity of centre of image.
<PRE>
Usage: mrcImageTransformSign
Options:
- [-i[nput] In (NULL )] :Essential :Input: MRC
- [-o[utput] Out (NULL )] :Essential :Output: MRC[default: ToSigned]
- [-toU[nsigned] ] :Optional :Flag: To Unsigned
- [-Offset Offset (0 )] :Optional :Input: Offset
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: MRC
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: MRC[default: ToSigned]
+ [-toU[nsigned] ] :Optional :Flag: To Unsigned
+ [-Offset Offset (0 ).as(Integer ) ] :Optional :Input: Offset
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageTranspose
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-M[ode2] Mode (0 )] :Optional :Mode2
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-M[ode2] Mode (0 ).as(Integer ) ] :Optional :Mode2
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageUnbentROI
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-r[oi] roiLine (NULL )... ] :Variable :
- [-x x (1.0 )] :Essential :Width :Source
- [-y y (1.0 )] :Optional :Height:Source
- [-W Width (1.0 )] :Optional :Width :Dst
- [-H Height (1.0 )] :Optional :Height:Dst
- [-cor Cor (360.0 )] :Optional :Correlation Window along Y-axis [A]
- [-S[hrink] Shrink (1 )] :Optional :When inputfile is shrinked:
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-r[oi] roiLine (NULL ).as(Real ) ... ] :Variable :
+ [-x x (1.0 ).as(Real ) ] :Essential :Width :Source
+ [-y y (1.0 ).as(Real ) ] :Optional :Height:Source
+ [-W Width (1.0 ).as(Real ) ] :Optional :Width :Dst
+ [-H Height (1.0 ).as(Real ) ] :Optional :Height:Dst
+ [-cor Cor (360.0 ).as(Real ) ] :Optional :Correlation Window along Y-axis [A]
+ [-S[hrink] Shrink (1 ).as(Integer ) ] :Optional :When inputfile is shrinked:
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcImageUnexpectedMassFromPDB
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-p[dbFile] InPDB (NULL )] :Essential :InputPDBDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-T[hres] Thres (0.0 )] :Essential :ThresHold
- [-D[ata] Data (0.0 )] :Essential :AssinedData
- [-M[ode] AtomMode (1 )] :Optional :AtomMode
- [-r[adius] radius (3.4 )] :Optional :Radius
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-p[dbFile] InPDB (NULL ).as(inFile ) ] :Essential :InputPDBDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-T[hres] Thres (0.0 ).as(Real ) ] :Essential :ThresHold
+ [-D[ata] Data (0.0 ).as(Real ) ] :Essential :AssinedData
+ [-M[ode] AtomMode (1 ).as(Integer ) ] :Optional :AtomMode
+ [-r[adius] radius (3.4 ).as(Real ) ] :Optional :Radius
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
>>> Mode:
0: Origin is BottomLeft.
1: Origin is Center.(Helix)
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImageUnsharpening</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageUnsharpening</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageUnsharpening
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input: mrcImage
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output: mrcImage
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+--UnsharpeningMode--
+0: 0 -1 0
+ -1 5 -1
+ 0 -1 0
+1:-1 -1 -1
+ -1 9 -1
+ -1 -1 -1
+2: 1 -2 1
+ -2 5 -2
+ 1 -2 1
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: mrcImageUntwist
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-dz[deltaz] dz (27.3 )] :Optional :deltaz(A)
- [-dp[deltaphi] dphi (13.84 )] :Optional :deltaphi(degree)
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-dz[deltaz] dz (27.3 ).as(Real ) ] :Optional :deltaz(A)
+ [-dp[deltaphi] dphi (13.84 ).as(Real ) ] :Optional :deltaphi(degree)
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImageVarianceAnalysis
Options:
- [-i[nput] In (NULL )] :Optional :In: InputList
- [-r[ef] Ref (NULL )] :Optional :Ref: InputList
- [-o[utput] Out (NULL )] :Optional :Output: Variance Probability
- [-v[arianceAnalysis] OutV (NULL )] :Optional :Output: Variance Analysis
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFileList ) ] :Optional :In: InputList
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :Output: Variance Probability
+ [-v[arianceAnalysis] OutV (NULL ).as(outFile ) ] :Optional :Output: Variance Analysis
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
-i inFileList
>>>>> Within inFileList
<PRE>
Usage: mrcImageVarianceMap
Options:
- [-i[nput] In (NULL )] :Optional :In: InputList
- [-I[nput] In2 (NULL )In2Var (NULL )In2N (0 )] :Optional :In: Input
- [-Nor[malizingParameter]NorA (0.0 )NorB (1.0 )] :Optional :In: A + B*x: NormalizingParameter
- [-r[ef] Ref (NULL )] :Optional :Ref: InputList
- [-R[ef] Ref2 (NULL )Ref2Var (NULL )Ref2N (0 )] :Optional :Ref: Input
- [-Nor[malizingParameter]RNorARef (0.0 )NorBRef (1.0 )] :Optional :In: A + B*x: NormalizingParameter for Ref
- [-I[and]R InAndRef2 (NULL )InAndRef2Var (NULL )InAndRef2N (0 )] :Optional :In and Ref: Input
- [-o[utput] Out (NULL )] :Optional :Output: Variance Probability
- [-v[arianceMap] OutV (NULL )] :Optional :Output: Variance Map
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFileList ) ] :Optional :In: InputList
+ [-I[nput] In2 (NULL ).as(inFile )
+ In2Var (NULL ).as(inFile )
+ In2N (0 ).as(Integer ) ] :Optional :In: Input
+ [-Nor[malizingParameter]NorA (0.0 ).as(Real )
+ NorB (1.0 ).as(Real ) ] :Optional :In: A + B*x: NormalizingParameter
+ [-r[ef] Ref (NULL ).as(inFileList ) ] :Optional :Ref: InputList
+ [-R[ef] Ref2 (NULL ).as(inFile )
+ Ref2Var (NULL ).as(inFile )
+ Ref2N (0 ).as(Integer ) ] :Optional :Ref: Input
+ [-Nor[malizingParameter]RNorARef (0.0 ).as(Real )
+ NorBRef (1.0 ).as(Real ) ] :Optional :In: A + B*x: NormalizingParameter for Ref
+ [-I[and]R InAndRef2 (NULL ).as(inFile )
+ InAndRef2Var (NULL ).as(inFile )
+ InAndRef2N (0 ).as(Integer ) ] :Optional :In and Ref: Input
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :Output: Variance Probability
+ [-v[arianceMap] OutV (NULL ).as(outFile ) ] :Optional :Output: Variance Map
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
---- Variance Map -----
-- Algorithm
<PRE>
Usage: mrcImageVolumeCalc
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-n[Molecule] nMolecule (1.0 )] :Optional :NumberOfMolecule
- [-M[olecularWeight] MolecularWeight (1.0 )] :Optional :MolecularWeight
- [-d[ensty] Density (1.35 )] :Optional :Density
- [-D[elta] Delta (5.0 )] :Optional :Delta[A]
- [-R[ange] MinVol (0.0 )MaxVol (200.0 )DeltaVol (10.0 )] :Optional :vol
- [-I[nverse] ] :Optional :Inverse
- [-format Format (ContourLevel(%3g): %g %lu)] :Optional :Format
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-n[Molecule] nMolecule (1.0 ).as(Real ) ] :Optional :NumberOfMolecule
+ [-M[olecularWeight] MolecularWeight (1.0 ).as(Real ) ] :Optional :MolecularWeight
+ [-d[ensty] Density (1.35 ).as(Real ) ] :Optional :Density
+ [-D[elta] Delta (5.0 ).as(Real ) ] :Optional :Delta[A]
+ [-R[ange] MinVol (0.0 ).as(Real )
+ MaxVol (200.0 ).as(Real )
+ DeltaVol (10.0 ).as(Real ) ] :Optional :vol
+ [-I[nverse] ] :Optional :Inverse
+ [-format Format (ContourLevel(%3g): %g %lu).as(StringAll ) ] :Optional :Format
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
-format
1st double # ContourLevel[%]
WxMax < x/Nx < Wx or 1-Wx < x/Nx < 1-WxMax : cos window
Wx < x/Nx < 1-Wx : 1
Wy and WyMax are also used for windowing in the similar manner.
-+0 : To Zero.
+ In general, this is called Tukey window.
3: Rectangle Window
4: Hanning Window
5: Hamming Window
6: Blackman Window
+7: Dolph-Chebyshev Window
+8: Kaiser Window
+ Wx, Wy corresponding to alpha. As alpha increases, window becomes narrower.
+9: Gauss Window
+10: Exponentail Window
+>> Boundary
+0 : To Zero.
+16: Contrast down around mean.
</PRE>
<PRE>
Usage: mrcImageZPad
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-r[max] r (0 )] :Optional :rmax = height of z window * 0.5 .
- [-w[idth] w (1 )] :Optional :Width of slope. For mode 1. Usually w>=3 is good enough.
- [-v[alue] v (0 )] :Optional :Value of out of threshold.
- [-Nx Nx (0 )] :Optional :Number of x.Default is inputfile.
- [-Ny Ny (0 )] :Optional :Number of y.Default is inputfile.
- [-Nz Nz (0 )] :Optional :Number of z.Default is inputfile.
- [-Floating ] :Optional :Floating
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-r[max] r (0 ).as(Real ) ] :Optional :rmax = height of z window * 0.5 .
+ [-w[idth] w (1 ).as(Real ) ] :Optional :Width of slope. For mode 1. Usually w>=3 is good enough.
+ [-v[alue] v (0 ).as(Real ) ] :Optional :Value of out of threshold.
+ [-Nx Nx (0 ).as(Integer ) ] :Optional :Number of x.Default is inputfile.
+ [-Ny Ny (0 ).as(Integer ) ] :Optional :Number of y.Default is inputfile.
+ [-Nz Nz (0 ).as(Integer ) ] :Optional :Number of z.Default is inputfile.
+ [-Floating ] :Optional :Floating
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- mode -----
0:Default: Out of threshold is avrage of threshold plain.
1:Mulplying cos function. Default: Out of threshold is avrage of threshold plain.
<PRE>
Usage: mrcImagepdbFileReduce
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-p[dbfile] Pdb (NULL )] :Essential :InputPdbFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-t[hreshold] Th (0 )] :Essential :Threshold
- [-r[adius] R (1 )] :Optional :Radius of Atom
- [-v[alue] Value (0 )] :Optional :Value for pixels in pdbFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-IT[interfacethreshold]ITh (0 )] :Optional :Threshold for interface recognition.
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-p[dbfile] Pdb (NULL ).as(inFile ) ] :Essential :InputPdbFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-t[hreshold] Th (0 ).as(Real ) ] :Essential :Threshold
+ [-r[adius] R (1 ).as(Real ) ] :Optional :Radius of Atom
+ [-v[alue] Value (0 ).as(Real ) ] :Optional :Value for pixels in pdbFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-IT[interfacethreshold]ITh (0 ).as(Real ) ] :Optional :Threshold for interface recognition.
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcImagesSinogramCorrelation
Options:
- [-I[nputList] In (NULL )] :Essential :InputDataFileList
- [-o[utput]H[eader] OutHeader (test )] :Optional :OutputDataFileHeader
- [-R[sults]d[irectoryname]Rd (Result )] :Optional :output results directory name
- [-N[ormalCorrelation]d[irectoryname]Nd (Normal )] :Optional :directory name of output normalcorrelation in results directory
- [-D[erivation]1[DCorrelation]d[irectoryname]D1d (Derivation1D)] :Optional :directory name of output derivation1Dcorrelation in results directory
- [-D[erivation]2[DCorrelation]d[irectoryname]D2d (Derivation2D)] :Optional :directory name of output derivation2Dcorrelation in results directory
- [-L[engthCorrelation]d[irectoryname]Ld (Length )] :Optional :directory name of output lengthcorrelation in results directory
- [-C[orrelation]E[xtension]CorrelationExtension(cor )] :Optional :output correlation file extension
- [-L[ist]E[xtension] ListExtension (list )] :Optional :output file list extension
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-N[ormalCorrelation]m[ode]Nmode (0 )] :Optional :
- [-D[erivation]1[DCorrelation]m[ode]D1mode (0 )] :Optional :
- [-D[erivation]2[DCorrelation]m[ode]D2mode (0 )] :Optional :
- [-L[engthCorrelation]m[ode]Lmode (0 )] :Optional :
- [-L[ength]T[hreshold]M[ode]LengthThresholdMode (0 )] :Optional :LengthThresholdMode
- [-L[ength]T[hreshold]M[ode]LengthThresholdRatio(0.25 )] :Optional :LengthThresholdRatio
- [-C[reate]M[ode] CM (0 )] :Optional :CreateMode
+ [-I[nputList] In (NULL ).as(inFileList ) ] :Essential :InputDataFileList
+ [-o[utput]H[eader] OutHeader (test ).as(String ) ] :Optional :OutputDataFileHeader
+ [-R[sults]d[irectoryname]Rd (Result ).as(String ) ] :Optional :output results directory name
+ [-N[ormalCorrelation]d[irectoryname]Nd (Normal ).as(String ) ] :Optional :directory name of output normalcorrelation in results directory
+ [-D[erivation]1[DCorrelation]d[irectoryname]D1d (Derivation1D).as(String ) ] :Optional :directory name of output derivation1Dcorrelation in results directory
+ [-D[erivation]2[DCorrelation]d[irectoryname]D2d (Derivation2D).as(String ) ] :Optional :directory name of output derivation2Dcorrelation in results directory
+ [-L[engthCorrelation]d[irectoryname]Ld (Length ).as(String ) ] :Optional :directory name of output lengthcorrelation in results directory
+ [-C[orrelation]E[xtension]CorrelationExtension(cor ).as(String ) ] :Optional :output correlation file extension
+ [-L[ist]E[xtension] ListExtension (list ).as(String ) ] :Optional :output file list extension
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-N[ormalCorrelation]m[ode]Nmode (0 ).as(Integer ) ] :Optional :
+ [-D[erivation]1[DCorrelation]m[ode]D1mode (0 ).as(Integer ) ] :Optional :
+ [-D[erivation]2[DCorrelation]m[ode]D2mode (0 ).as(Integer ) ] :Optional :
+ [-L[engthCorrelation]m[ode]Lmode (0 ).as(Integer ) ] :Optional :
+ [-L[ength]T[hreshold]M[ode]LengthThresholdMode (0 ).as(Integer ) ] :Optional :LengthThresholdMode
+ [-L[ength]T[hreshold]M[ode]LengthThresholdRatio(0.25 ).as(Real ) ] :Optional :LengthThresholdRatio
+ [-C[reate]M[ode] CM (0 ).as(Integer ) ] :Optional :CreateMode
----- create mode -----
-CM : 0 : image of correlation and list
<PRE>
Usage: mrcImagestoRef
Options:
- [-I[nput array of file]In (stdin )] :Optional :InputDataFiles
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-I[nput array of file]In (stdin ).as(inFileListNoOpen ) ] :Optional :InputDataFiles
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
This program packs same size images to no header reference file.</PRE>
</BODY>
<PRE>
Usage: mrcImateToPointsSet
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcInfoSet
Options:
- [-i[nput] In (NULL )] :Essential :InputMrcFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-Length Lengthx (2.5 )Lengthy (2.5 )Lengthz (2.5 )] :Optional :Length[A]
- [-Fixed ] :Optional :Fixed Values in mrcImageHeader are fixed.
- [-Interactive ] :Optional :Interactive(CUI)
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputMrcFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-Length Lengthx (2.5 ).as(Real )
+ Lengthy (2.5 ).as(Real )
+ Lengthz (2.5 ).as(Real ) ] :Optional :Length[A]
+ [-Fixed ] :Optional :Fixed Values in mrcImageHeader are fixed.
+ [-Interactive ] :Optional :Interactive(CUI)
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcMask
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-s[ize] sizeX (1 )sizeY (1 )] :Optional :Mask Size (Odd Only) /pixel
- [-v[ector]1 v1x (1 )v1y (0 )] :Essential :Vector1(/A):x y
- [-v[ector]2 v2x (0 )v2y (1 )] :Optional :Vector2(/A):x y
- [-in[initial number] inum (1 )] :Optional :Initialn number of data to cut out.For 1D only.
- [-fn[final number] num (0 )] :Optional :Final number of data to cut out.For 1D only.Default:All.
- [-en[extra number] exnum (0 )] :Optional :Extra number of data to cut out.For mode 2 only
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-s[ize] sizeX (1 ).as(Integer )
+ sizeY (1 ).as(Integer ) ] :Optional :Mask Size (Odd Only) /pixel
+ [-v[ector]1 v1x (1 ).as(Real )
+ v1y (0 ).as(Real ) ] :Essential :Vector1(/A):x y
+ [-v[ector]2 v2x (0 ).as(Real )
+ v2y (1 ).as(Real ) ] :Optional :Vector2(/A):x y
+ [-in[initial number] inum (1 ).as(Integer ) ] :Optional :Initialn number of data to cut out.For 1D only.
+ [-fn[final number] num (0 ).as(Integer ) ] :Optional :Final number of data to cut out.For 1D only.Default:All.
+ [-en[extra number] exnum (0 ).as(Integer ) ] :Optional :Extra number of data to cut out.For mode 2 only
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcMeanYlinePos
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-w[idth] width (-1 )] :Optional :GetMeanWidth
- [-o[utput] Out (stdout )] :Optional :Output
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-w[idth] width (-1 ).as(Integer ) ] :Optional :GetMeanWidth
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcMirrorImageCreate
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcRadon2Dto3D
Options:
- [-I[nput] In2 (NULL )] :Essential :InputDataFileList
- [-I[nput]b[efore] InBefore (NULL )] :Optional :InputDataFileListBefore
- [-i[nput]b[efore] inbefore (NULL )] :Optional :InputDataFileBeforeData: mrcImageRadon3D
- [-i[nput]w[eight]b[efore]inWbefore (NULL )] :Optional :InputWeightDataFileBeforeData: mrcImageRadon3D
- [-o[utput] Out (NULL )] :Essential :OutputDataFile: radon3D
- [-o[utput]w[eight] OutW (NULL )] :Essential :OutputDataFile: weight
- [-dp dp (2.0 )] :Essential :Input: deltaP
- [-dtheta dtheta (1 )] :Essential :Input: deltaTheta
- [-dphi dphi (1 )] :Essential :Input: deltaPhi
- [-T[hreshold] T (1.0 )] :Optional :Threshold
- [-InterpolationMode InterpolationMode (0 )] :Optional :InterpolationMode
- [-m[ode] mode (0 )] :Optional :Radon2Dto3D Intepolation Mode
+ [-I[nput] In2 (NULL ).as(inFileList ) ] :Essential :InputDataFileList
+ [-I[nput]b[efore] InBefore (NULL ).as(inFileList ) ] :Optional :InputDataFileListBefore
+ [-i[nput]b[efore] inbefore (NULL ).as(inFile ) ] :Optional :InputDataFileBeforeData: mrcImageRadon3D
+ [-i[nput]w[eight]b[efore]inWbefore (NULL ).as(inFile ) ] :Optional :InputWeightDataFileBeforeData: mrcImageRadon3D
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile: radon3D
+ [-o[utput]w[eight] OutW (NULL ).as(outFile ) ] :Essential :OutputDataFile: weight
+ [-dp dp (2.0 ).as(Real ) ] :Essential :Input: deltaP
+ [-dtheta dtheta (1 ).as(Real ) ] :Essential :Input: deltaTheta
+ [-dphi dphi (1 ).as(Real ) ] :Essential :Input: deltaPhi
+ [-T[hreshold] T (1.0 ).as(Real ) ] :Optional :Threshold
+ [-InterpolationMode InterpolationMode (0 ).as(Integer ) ] :Optional :InterpolationMode
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Radon2Dto3D Intepolation Mode
----- mode -----
0 = NearestNeighbor
<PRE>
Usage: mrcRefCorEstimate
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode 0:Alignment is just. 1:Alignment is just.To display distance of max.2:No alignment 3:No alignment and alpha of reference is 180.
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode 0:Alignment is just. 1:Alignment is just.To display distance of max.2:No alignment 3:No alignment and alpha of reference is 180.
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcRefCorModify
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode:0 Absolute Value 1: The max of y line is normalize to 1.(Absolute Value)
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode:0 Absolute Value 1: The max of y line is normalize to 1.(Absolute Value)
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcRefCoreGet
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-C[utoff] Cutoff (0 )] :Optional :Cutoff
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode:0 If |Pixel of Image| < Cutoff ,|Pixel of Image|=0 ,1:If |Pixel of Image| < Cutoff*SqrAvr ,|Pixel of Image|=0
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-C[utoff] Cutoff (0 ).as(Real ) ] :Optional :Cutoff
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode:0 If |Pixel of Image| < Cutoff ,|Pixel of Image|=0 ,1:If |Pixel of Image| < Cutoff*SqrAvr ,|Pixel of Image|=0
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcRefCorrelation
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-r[eference] In2 (NULL )] :Optional :For Mode1=1 only:ReferenceDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-r[eference] In2 (NULL ).as(inFile ) ] :Optional :For Mode1=1 only:ReferenceDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :
Mode1 0:AutoCorrelation
1:CrossCorrelation
- [-M[ode] mode2 (0 )] :Optional :
+ [-M[ode] mode2 (0 ).as(Integer ) ] :Optional :
Mode2 0:All is to be calculated.
1:Pick up at random
2:Calculate only Omega=0,Alpha=0
- [-n[umber] number (NULL )] :Optional :For mode 1 only. Number of points to pick up at random. Defalt:Data size along z axis of inputfile / 10
+ [-n[umber] number (NULL ).as(Integer ) ] :Optional :For mode 1 only. Number of points to pick up at random. Defalt:Data size along z axis of inputfile / 10
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcRefCorrelationConv
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode 0:phi,omega 1:phi,alpha 2:omega,alpha
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode 0:phi,omega 1:phi,alpha 2:omega,alpha 3:For one point
+ [p[oint] Phi (0 ).as(Integer )
+ Omega (0 ).as(Integer )
+ Alpha (0 ).as(Integer ) ] :Optional :For mode 3 only:Central point of Correlatin.(Phi,Omega,Alpha)
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcRefEstimate
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcRefFFTConvert
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode 0:Fourier translation 1:Create Fourier phase image
+ [-p[ower] Power (1 ).as(Real ) ] :Optional :For mode 1 only: Use F/( |F|^p ) to create fourier phase image
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcRefHeaderCreate
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-p[osition] iP (0 )iW (0 )iA (0 )] :Optional :Position of Center of model creation. Phi(degree) ,Omega(degree) ,Alpha(degree)
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-p[osition] iP (0 ).as(Real )
+ iW (0 ).as(Real )
+ iA (0 ).as(Real ) ] :Optional :Position of Center of model creation. Phi(degree) ,Omega(degree) ,Alpha(degree)
:Omega and Alpha range must be around 0 or 180.
- [-w[idth] Wp (360 )Ww (10 )Wa (10 )] :Optional :Width of Phi(degree,plus minus) ,Omega(degree,plus minus) ,Alpha(degree,plus minus)
- [-d[elta] Dp (5 )Dw (5 )Da (5 )] :Optional :Interval of model creation(degree) Phi(around Z axis),Omega(Y axis),Alpha(X axis)
- [-s[tart]y Sy (0 )] :Optional :Start y: For mode 1 only
- [-e[end]y Ey (0 )] :Optional :End y: For mode 1 only. Default is Ny-1
- [-refsize Refsize (0 )] :Optional :Size of reference data.
- [-m[ode] mode (0 )] :Optional :Mode
+ [-w[idth] Wp (360 ).as(Real )
+ Ww (10 ).as(Real )
+ Wa (10 ).as(Real ) ] :Optional :Width of Phi(degree,plus minus) ,Omega(degree,plus minus) ,Alpha(degree,plus minus)
+ [-d[elta] Dp (5 ).as(Real )
+ Dw (5 ).as(Real )
+ Da (5 ).as(Real ) ] :Optional :Interval of model creation(degree) Phi(around Z axis),Omega(Y axis),Alpha(X axis)
+ [-s[tart]y Sy (0 ).as(Integer ) ] :Optional :Start y: For mode 1 only
+ [-e[end]y Ey (0 ).as(Integer ) ] :Optional :End y: For mode 1 only. Default is Ny-1
+ [-refsize Refsize (0 ).as(Integer ) ] :Optional :Size of reference data.
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcRefHighPassFilter
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-h[alf]v[alue]p[oint]hvp (1.0 )] :Optional :HalfValuePoint
- [-w[idth] width (1.0 )] :Optional :WidthOfDumping
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-h[alf]v[alue]p[oint]hvp (1.0 ).as(Real ) ] :Optional :HalfValuePoint
+ [-w[idth] width (1.0 ).as(Real ) ] :Optional :WidthOfDumping
>>> Mode <<<<
1: Step filter : required argumnent: -hvp
2: Cos filter : required argumnent: -hvp -w
<PRE>
Usage: mrcRefImageCorrelation
Options:
- [-i[nput] In (NULL )] :Optional :InputDataFile
- [-r[eference] Ref (NULL )] :Essential :ReferenceDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-I[nput array of file]InArray (stdin )] :Optional :InputDataFiles
+ [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputDataFile
+ [-r[eference] Ref (NULL ).as(inFile ) ] :Essential :ReferenceDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-I[nput array of file]InArray (stdin ).as(inFileList ) ] :Optional :InputDataFiles
+ [-z[position] z (0 ).as(Integer ) ] :Optional :z position of reference file to correlate.For mode 1 only
----- Additional Usage -----
mode 0: To find the images in the reference file of min and max correlation. Correlation is calclated in the real space.
mode 1: To calculate the correlation between one image of the reference file and input file. The calculation is performed in the fourier space and the output is a mrc image file. option z is needed.
<PRE>
Usage: mrcRefImageOmegaCorrelation
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcRefImagepwzCorEstimate
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcRefImagepwzCorModify
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-nr[Ny of reference file]Nry (0 )] :Optional :Needed only for old format
- [-mag[nification] mag (1 )] :Optional :Ratio of new magnification to old magnification
- [-s[hift] shift (0.0 )] :Optional :y-shift[pixel]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-M[ode2] mode2 (0 )] :Optional :Mode2
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-nr[Ny of reference file]Nry (0 ).as(Integer ) ] :Optional :Needed only for old format
+ [-mag[nification] mag (1 ).as(Real ) ] :Optional :Ratio of new magnification to old magnification
+ [-s[hift] shift (0.0 ).as(Real ) ] :Optional :y-shift[pixel]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-M[ode2] mode2 (0 ).as(Integer ) ] :Optional :Mode2
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcRefImagepwzCorPeakFind
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-N[unber] N (20 )] :Optional :Number of peaks
- [-dN[delta number] dN (5 )] :Optional :Number of template shift
- [-d[elta]p[hi] dp (166.1538462)] :Optional :Delta phi(Degree)
- [-d[elta]z dz (27.3 )] :Optional :Delta z(A)
- [-l[ength] length (1000 )] :Optional :Length to extract.:mode 2 only
- [-div[ision] div (1 )] :Optional :Number to division.:mode 2 only
- [-m[ode] mode (0 )] :Optional :Mode
- [-M[ode2] mode2 (0 )] :Optional :Mode2
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-N[unber] N (20 ).as(Integer ) ] :Optional :Number of peaks
+ [-dN[delta number] dN (5 ).as(Integer ) ] :Optional :Number of template shift
+ [-d[elta]p[hi] dp (166.1538462).as(Real ) ] :Optional :Delta phi(Degree)
+ [-d[elta]z dz (27.3 ).as(Real ) ] :Optional :Delta z(A)
+ [-l[ength] length (1000 ).as(Integer ) ] :Optional :Length to extract.:mode 2 only
+ [-div[ision] div (1 ).as(Integer ) ] :Optional :Number to division.:mode 2 only
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-M[ode2] mode2 (0 ).as(Integer ) ] :Optional :Mode2
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcRefImagepwzCorSmoothing
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-N[unber] N (20 )] :Optional :Number of peaks
- [-d[elta]p[hi] dp (166.1538462)] :Optional :Delta phi(Degree)
- [-d[elta]z dz (27.3 )] :Optional :Delta z(A)
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-N[unber] N (20 ).as(Integer ) ] :Optional :Number of peaks
+ [-d[elta]p[hi] dp (166.1538462).as(Real ) ] :Optional :Delta phi(Degree)
+ [-d[elta]z dz (27.3 ).as(Real ) ] :Optional :Delta z(A)
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcRefImagepwzCorrelation
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-r[eference] Ref (NULL )] :Optional :ReferenceFile
- [-dy[deltay] dy (1 )] :Optional :Deltay
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-M[ode2] mode2 (0 )] :Optional :Mode2
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-r[eference] Ref (NULL ).as(inFile ) ] :Optional :ReferenceFile
+ [-dy[deltay] dy (1 ).as(Integer ) ] :Optional :Deltay
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-M[ode2] mode2 (0 ).as(Integer ) ] :Optional :Mode2
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcRefImagepwzCorrelationByFFT
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcRefImagexaFit
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-ix[initial x] ix (NULL )] :Optional :Initial x(pixel)
- [-ia[initial alpha] ia (0 )] :Optional :Initial alpha(degree)
- [-r[eference] Ref (NULL )] :Optional :ReferenceFile
- [-dy[deltay] Dy (10 )] :Optional :Deltay
- [-xrange xrange (3 )] :Optional :x range to search (pixel)
- [-arange arange (2 )] :Optional :alpha range to search (degree)
- [-v[alue] Value (1 )] :Optional :Value of Peak Pixel :for mode2
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-M[ode2] mode2 (0 )] :Optional :Mode2
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-ix[initial x] ix (NULL ).as(Integer ) ] :Optional :Initial x(pixel)
+ [-ia[initial alpha] ia (0 ).as(Real ) ] :Optional :Initial alpha(degree)
+ [-r[eference] Ref (NULL ).as(inFile ) ] :Optional :ReferenceFile
+ [-dy[deltay] Dy (10 ).as(Integer ) ] :Optional :Deltay
+ [-xrange xrange (3 ).as(Integer ) ] :Optional :x range to search (pixel)
+ [-arange arange (2 ).as(Integer ) ] :Optional :alpha range to search (degree)
+ [-v[alue] Value (1 ).as(Real ) ] :Optional :Value of Peak Pixel :for mode2
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-M[ode2] mode2 (0 ).as(Integer ) ] :Optional :Mode2
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcRefLowPassFilter
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-h[alf]v[alue]p[oint]hvp (1.0 )] :Optional :HalfValuePoint
- [-w[idth] width (1.0 )] :Optional :WidthOfDumping
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-h[alf]v[alue]p[oint]hvp (1.0 ).as(Real ) ] :Optional :HalfValuePoint
+ [-w[idth] width (1.0 ).as(Real ) ] :Optional :WidthOfDumping
>>> Mode <<<<
1: Step filter : required argumnent: -hvp
2: Cos filter : required argumnent: -hvp -w
<PRE>
Usage: mrcRefNoiseAdd
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-s[trength] Noise (1.0 )] :Optional :Strength of Noise.Unit is standard deviation of input reference.
- [-m[ode] mode (0 )] :Optional :Mode
- [-h[igh] H (0 )] :Optional :High threshold to calclate S.D. Default is max of input file.
- [-l[ow] L (0 )] :Optional :Low threshold to calclate S.D. Default is min of input file.
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-s[trength] Noise (1.0 ).as(Real ) ] :Optional :Strength of Noise.Unit is standard deviation of input reference.
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-h[igh] H (0 ).as(Real ) ] :Optional :High threshold to calclate S.D. Default is max of input file.
+ [-l[ow] L (0 ).as(Real ) ] :Optional :Low threshold to calclate S.D. Default is min of input file.
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcRefNormalizing
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcRefPhaseImageCreate
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-p[ower] Power (1 )] :Optional :Use (|F|^p ) to create fourier phase image
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-C[utoff] Cutoff (-1.0 )] :Optional :Mode 0:If |F|<Cutoff ,this pixel is not used.Default:Mean/10
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-p[ower] Power (1 ).as(Real ) ] :Optional :Use (|F|^p ) to create fourier phase image
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-C[utoff] Cutoff (-1.0 ).as(Real ) ] :Optional :Mode 0:If |F|<Cutoff ,this pixel is not used.Default:Mean/10
Mode 1:|F|<Cutoff*Mean is used to cut.Default:0.1
</PRE>
</BODY>
<PRE>
Usage: mrcRefSmoothing
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-sx sx (3 )] :Optional :x of Kernel Size
- [-sy sy (3 )] :Optional :y of Kernel Size
- [-sz sz (3 )] :Optional :z of Kernel Size
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-sx sx (3 ).as(Integer ) ] :Optional :x of Kernel Size
+ [-sy sy (3 ).as(Integer ) ] :Optional :y of Kernel Size
+ [-sz sz (3 ).as(Integer ) ] :Optional :z of Kernel Size
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: mrcRefz1ImageCorrelation
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-r[eference] Ref (NULL )] :Optional :ReferenceFile
- [-z[position] z (0 )] :Optional :z position of reference file to correlate
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-r[eference] Ref (NULL ).as(inFile ) ] :Optional :ReferenceFile
+ [-z[position] z (0 ).as(Integer ) ] :Optional :z position of reference file to correlate
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcSinogramFET
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-ch[eck] OutC (NULL )] :Optional :OutputDataForCheckByEye
- [-sm[ooth] sm (1 )] :Optional :SmoothingFilter
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-ch[eck] OutC (NULL ).as(outFile ) ] :Optional :OutputDataForCheckByEye
+ [-sm[ooth] sm (1 ).as(Integer ) ] :Optional :SmoothingFilter
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
-sm : move range of column smoothing by moving-average
</PRE>
<PRE>
Usage: mrcSinogramFETcalcSDforNormalize
Options:
- [-i[nput] In (NULL )] :Optional :InputFETDataFile
- [-s[elect] Sm (1 )] :Optional :selectFETfile
- [-l[ibrary] Libl (NULL )] :Essential :SDlibraryFile
- [-o[utput] Out (NULL )] :Optional :OutputSDdataFile
- [-o[ut]w[eight] OW (NULL )] :Optional :OutputWeightdataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputFETDataFile
+ [-s[elect] Sm (1 ).as(Integer ) ] :Optional :selectFETfile
+ [-l[ibrary] Libl (NULL ).as(inFile ) ] :Essential :SDlibraryFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputSDdataFile
+ [-o[ut]w[eight] OW (NULL ).as(outFile ) ] :Optional :OutputWeightdataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
mode 0: SDfile writeout from liblary file
Library(option -l) is Essential
<PRE>
Usage: mrcSinogramFETcalcWeight
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-c[ommon]l[ine] InC (NULL )] :Essential :inputCommonLineFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-c[ommon]l[ine] InC (NULL ).as(inFile ) ] :Essential :inputCommonLineFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: mrcSinogramFETcorrelationMap
Options:
- [-i[nput]1 In1 (NULL )] :Essential :InputSinogramFETFile1
- [-i[nput]2 In2 (NULL )] :Essential :InputSinogramFETFile2
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-w[eight] Weight (NULL )] :Optional :WeightDataFile mrcFormat
- [-s[tandard]d[eviation]SD (NULL )] :Optional :readSDfileForNormalize
- [-n[orm]m[ode] NM (0 )] :Optional :normalizemode
- [-c[alc]mode CMode (0 )] :Optional :calculateMode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput]1 In1 (NULL ).as(inFile ) ] :Essential :InputSinogramFETFile1
+ [-i[nput]2 In2 (NULL ).as(inFile ) ] :Essential :InputSinogramFETFile2
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-w[eight] Weight (NULL ).as(inFile ) ] :Optional :WeightDataFile mrcFormat
+ [-s[tandard]d[eviation]SD (NULL ).as(inFile ) ] :Optional :readSDfileForNormalize
+ [-n[orm]m[ode] NM (0 ).as(Integer ) ] :Optional :normalizemode
+ [-c[alc]mode CMode (0 ).as(Integer ) ] :Optional :calculateMode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
mode 0 : default, normal distance correlation
mode 1 : average of counter pixel presents same line
<PRE>
Usage: mrcSinogramFETnormalizedMap
Options:
- [-i[nput] In (NULL )] :Essential :InputFETlistFile
- [-o[utput] OutFET (NULL )] :Essential :OutputFETmrcformat
- [-cl[ine]List comList (NULL )] :Optional :commonlineList
- [-O[utput] OutMAP (NULL )] :Optional :OutputMAPmrcformat
- [-w[eight] Weight (NULL )] :Optional :WeightForDistanceCalc
- [-atm[ode] AAtm (1 )] :Optional :AAtestmode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputFETlistFile
+ [-o[utput] OutFET (NULL ).as(outFile ) ] :Essential :OutputFETmrcformat
+ [-cl[ine]List comList (NULL ).as(inFile ) ] :Optional :commonlineList
+ [-O[utput] OutMAP (NULL ).as(outFile ) ] :Optional :OutputMAPmrcformat
+ [-w[eight] Weight (NULL ).as(inFile ) ] :Optional :WeightForDistanceCalc
+ [-atm[ode] AAtm (1 ).as(Integer ) ] :Optional :AAtestmode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
"-O" option do not work at Oct.24,2007
aatestmode 0: default, check whole distance
<PRE>
Usage: mrcSinogramFETreferredCorrelation
Options:
- [-i[nput] In (NULL )] :Essential :InputFETDataFileList
- [-o[utput] Out (NULL )] :Essential :OutputEulerAngleDataFileList
- [-i[nput]Ref InR (NULL )] :Essential :InputReferenceFETDataFileList
- [-i[nput]Euler InE (NULL )] :Essential :InputEulerAngleDataFile
- [-n[ormalize]m[ode] NM (0 )] :Optional :normalizeMode
- [-o[utputList]m[ode] OM (2 )] :Optional :outputListMode
- [-t[op]n[um] TN (10 )] :Optional :top number
- [-refR[ange] RR (15 )] :Optional :reference select Range
- [-w[eight] WEIGHT (NULL )] :Optional :CorrelationCalcWeight
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputFETDataFileList
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputEulerAngleDataFileList
+ [-i[nput]Ref InR (NULL ).as(inFile ) ] :Essential :InputReferenceFETDataFileList
+ [-i[nput]Euler InE (NULL ).as(inFile ) ] :Essential :InputEulerAngleDataFile
+ [-n[ormalize]m[ode] NM (0 ).as(Integer ) ] :Optional :normalizeMode
+ [-o[utputList]m[ode] OM (2 ).as(Integer ) ] :Optional :outputListMode
+ [-t[op]n[um] TN (10 ).as(Integer ) ] :Optional :top number
+ [-refR[ange] RR (15 ).as(Integer ) ] :Optional :reference select Range
+ [-w[eight] WEIGHT (NULL ).as(inFile ) ] :Optional :CorrelationCalcWeight
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
Input EulerAngleDataFile example
<PRE>
Usage: mrcSinogramFETsmoothParameterMatching
Options:
- [-i[nput] In (NULL )] :Essential :InputFileList
- [-i[nput]s[tandard] InSTD (NULL )] :Essential :StandardSinogramFile
- [-o[utput] Out (NULL )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputFileList
+ [-i[nput]s[tandard] InSTD (NULL ).as(inFile ) ] :Essential :StandardSinogramFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: pdb2SketchMacro
Options:
- [-i[nput] In (stdin )] :Optional :InputDataFile
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-MolName MolName (TS )] :Optional :MolecularName[prefer to <=2]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (15 )] :Optional :Mode
+ [-i[nput] In (stdin ).as(inFile ) ] :Optional :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-MolName MolName (TS ).as(String ) ] :Optional :MolecularName[prefer to <=2]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (15 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
>>>> -m
1 : Helix sketched with spirals
<PRE>
Usage: pdb2bender
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: pdb2mrc
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Optional :OutputDataFile(3D)
- [-nx nx (1 )] :Optional :Pixel[Def:]
- [-ny ny (1 )] :Optional :Pixel[Def:]
- [-nz nz (1 )] :Optional :Pixel[Def:]
- [-Sx[tart] Startx (0.0 )] :Optional :Startx[A]
- [-Sy[tart] Starty (0.0 )] :Optional :Starty[A]
- [-Sz[tart] Startz (0.0 )] :Optional :Startz[A]
- [-dx dx (2.5 )] :Optional :dx
- [-dy dy (2.5 )] :Optional :dy
- [-dz dz (2.5 )] :Optional :dz
- [-w[eight] Weight (1.0 )] :Optional :Weight
- [-sig[ma] Sigma (0.0 )] :Optional :Sigma[A]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile(3D)
+ [-nx nx (1 ).as(Integer ) ] :Optional :Pixel[Def:]
+ [-ny ny (1 ).as(Integer ) ] :Optional :Pixel[Def:]
+ [-nz nz (1 ).as(Integer ) ] :Optional :Pixel[Def:]
+ [-Sx[tart] Startx (0.0 ).as(Real ) ] :Optional :Startx[A]
+ [-Sy[tart] Starty (0.0 ).as(Real ) ] :Optional :Starty[A]
+ [-Sz[tart] Startz (0.0 ).as(Real ) ] :Optional :Startz[A]
+ [-dx dx (2.5 ).as(Real ) ] :Optional :dx
+ [-dy dy (2.5 ).as(Real ) ] :Optional :dy
+ [-dz dz (2.5 ).as(Real ) ] :Optional :dz
+ [-w[eight] Weight (1.0 ).as(Real ) ] :Optional :Weight
+ [-sig[ma] Sigma (0.0 ).as(Real ) ] :Optional :Sigma[A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
>>> mode
mode: DensityMode
0: Same Gaussian
-/bin/bash: pdb2mrc2d: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdb2mrc2d</TITLE>
+</HEAD>
+<BODY>
+<H1>pdb2mrc2d</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdb2mrc2d
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile(2D)
+ [-O[utput] Out3D (NULL ).as(outFile ) ] :Optional :OutputDataFile(3D)
+ [-d[elta] dx (5.0 ).as(Real )
+ dy (5.0 ).as(Real ) ] :Essential :delta: dx[A] dy[A]
+ [-s[tart] sx (0.0 ).as(Real )
+ sy (0.0 ).as(Real ) ] :Optional :start: startx[A] starty[A]: When -s was not set, image centre is the origin(0,0,0)
+ [-n[umber] nx (0 ).as(Integer )
+ ny (0 ).as(Integer ) ] :Essential :N: nx ny (image size)
+ [-Rot[ation] rotnx (1 ).as(Integer )
+ rotny (1 ).as(Integer ) ] :Optional :rotnx rotny
+ [-S[tart] srotx (0.0 ).as(Real )
+ sroty (0.0 ).as(Real )
+ srotz (0.0 ).as(Real ) ] :Optional :start(rotx roty rotz):ZXY
+ [-startE[uler]A[ngle]sRotMode (YOYS ).as(String )
+ sRot1 (0.0 ).as(Real )
+ sRot2 (0.0 ).as(Real )
+ sRot3 (0.0 ).as(Real ) ] :Optional :EulerAngle: Start Angle
+ [-E[uler]A[ngle]Mode RotMode (YOYS ).as(String ) ] :Optional :RotationMode
+ [-E[uler]A[ngle]Rot1 dRot1 (5.0 ).as(Real )
+ minRot1 (0.0 ).as(Real )
+ maxRot1 (180.0 ).as(Real ) ] :Optional :FirstRotation
+ [-E[uler]A[ngle]Rot2 dRot2 (5.0 ).as(Real )
+ minRot2 (0.0 ).as(Real )
+ maxRot2 (180.0 ).as(Real ) ] :Optional :SecondRotation
+ [-w[eight] Weight (1.0 ).as(Real ) ] :Optional :weight
+ [-sig[ma] Sigma (0.0 ).as(Real ) ] :Optional :Sigma[A]:Atom radius
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-cuda cudaDeviceID (0 ).as(Integer ) ] :Optional :UseCuda
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode: 0 Merc; 1: Earth
+----- Attention1 -----
+If both of -s and -startEA, first -s and second -startEA will be performed
+----- Attention2 -----
+Bug fixed: rotation around x-axis. + is changed to -
+----- Mode -----
+1: 0: equal angle 1: equal area
+2: 0: Mercatol 1: Morwide
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdb2mrc2dWithCTF: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdb2mrc2dWithCTF</TITLE>
+</HEAD>
+<BODY>
+<H1>pdb2mrc2dWithCTF</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdb2mrc2dWithCTF
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: PDB
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: MRC
+ [-N Nx (2048 ).as(Integer )
+ Ny (2048 ).as(Integer ) ] :Optional :Input: Nx Ny [pixel]
+ [-d dx (1.72 ).as(Real )
+ dy (1.72 ).as(Real ) ] :Optional :Input: dx dy [A]
+ [-Centre cx (0 ).as(Real )
+ cy (0 ).as(Real )
+ cz (0 ).as(Real ) ] :Optional :Input: CentreX CentreY [A]
+ [-n nx (64 ).as(Integer )
+ ny (64 ).as(Integer ) ] :Optional :Input: nx ny for subimage [pixel]
+ [-kV kV (200. ).as(Real ) ] :Optional :kV
+ [-Cs Cs (1.7 ).as(Real ) ] :Optional :Cs
+ [-d[e]f[ocus] Defocus (10000 ).as(Real ) ] :Optional :Defocus [A] at z = 0
+ [-A[overP] AoverP (0.07 ).as(Real ) ] :Optional :AoverP
+ [-Ain Ain (0.2 ).as(Real ) ] :Optional :Beta: IlluminationAngle [mrad]
+ [-ctfMode ctfMode (33 ).as(Integer ) ] :Optional :ctfMode
+ [-E[uler]A[ngle] EulerAngle (XEYS ).as(String )
+ Rot1 (0 ).as(Real )
+ Rot2 (0 ).as(Real )
+ Rot3 (0 ).as(Real ) ] :Optional :EulerAngle: [degree]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: pdb2ucd
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: pdbAtomSection
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-i[nput of ]f[lags] InFlags (NULL )] :Optional :InputFlagsFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-dist[ance] distance (2.5 )] :Optional :DistanceOfSections
- [-zmin[imum] zmin (0.0 )] :Optional :Minimum of Z
- [-zmax[imum] zmax (90.0 )] :Optional :Maximum of Z
- [-f[lag]m[ode] flagMode (13 )] :Optional :flag mode
- [-r[adius] radius (1.0 )] :Optional :radius of the circle
- [-c[ircle]l[ine]w[idth]clinewidth (0.1 )] :Optional :circle line width
- [-p[eptide bond]l[ine]w[idth]plinewidth (0.1 )] :Optional :peptide bond line width
- [-fontsize fontsize (2.0 )] :Optional :font size
- [-A[bsolute]S[caleofPSFile]scale (1.0 )] :Optional :absolute scale of PS file (-AS 1 := 1 mm/A)
- [-shiftx shiftx (0.0 )] :Optional :pdb Shift x [A]
- [-shifty shifty (0.0 )] :Optional :pdb Shift y [A]
- [-shiftz shiftz (0.0 )] :Optional :pdb Shift z [A]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i[nput of ]f[lags] InFlags (NULL ).as(inFile ) ] :Optional :InputFlagsFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-dist[ance] distance (2.5 ).as(Real ) ] :Optional :DistanceOfSections
+ [-zmin[imum] zmin (0.0 ).as(Real ) ] :Optional :Minimum of Z
+ [-zmax[imum] zmax (90.0 ).as(Real ) ] :Optional :Maximum of Z
+ [-f[lag]m[ode] flagMode (13 ).as(Integer ) ] :Optional :flag mode
+ [-r[adius] radius (1.0 ).as(Real ) ] :Optional :radius of the circle
+ [-c[ircle]l[ine]w[idth]clinewidth (0.1 ).as(Real ) ] :Optional :circle line width
+ [-p[eptide bond]l[ine]w[idth]plinewidth (0.1 ).as(Real ) ] :Optional :peptide bond line width
+ [-fontsize fontsize (2.0 ).as(Real ) ] :Optional :font size
+ [-A[bsolute]S[caleofPSFile]scale (1.0 ).as(Real ) ] :Optional :absolute scale of PS file (-AS 1 := 1 mm/A)
+ [-shiftx shiftx (0.0 ).as(Real ) ] :Optional :pdb Shift x [A]
+ [-shifty shifty (0.0 ).as(Real ) ] :Optional :pdb Shift y [A]
+ [-shiftz shiftz (0.0 ).as(Real ) ] :Optional :pdb Shift z [A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
<PRE>
Usage: pdbCAOnly
Options:
- [-i[nput] In (NULL )] :Essential :Input: pdb
- [-o[utput] Out (NULL )] :Optional :Output: pdb
- [-o[utput]Coord OutCoord (NULL )] :Optional :Output: x,y,z
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: pdb
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :Output: pdb
+ [-o[utput]Coord OutCoord (NULL ).as(outFile ) ] :Optional :Output: x,y,z
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
-/bin/bash: pdbChargeFit: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbChargeFit</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbChargeFit</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbChargeFit
+Options:
+ [-i[nput]f[ixed pdb] InFix (NULL ).as(inFile ) ] :Essential :InputFixedPdbFile
+ [-i[nput]m[oved pdb] InMove (NULL ).as(inFile ) ] :Essential :InputMovedPdbFile
+ [-o[utput] OutTxt (NULL ).as(outFile ) ] :Essential :OutputTextFile
+ [-s[ymmetry of helix(degree/A)]symmetry (0.47096 ).as(Real ) ] :Optional :default: 13/28
+ [-zmin zmin (-28 ).as(Real ) ] :Optional :minimum z
+ [-zmax zmax (28 ).as(Real ) ] :Optional :maximum z
+ [-zDel[ta] zDel (1 ).as(Real ) ] :Optional :delta z
+ [-mind[istance] mind (1 ).as(Real ) ] :Optional :set atoms distance to mind
+ [-maxd[istance] maxd (5 ).as(Real ) ] :Optional :ignore atoms distance
+ [-a[xis coordinate] axisX (70 ).as(Real )
+ axisY (70 ).as(Real ) ] :Optional :(x, y)
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Algorythm -----
+score = Sum(1/SQR(length))
+, where length is the set of length between charged atoms
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: pdbCoordAdd
Options:
- [-i[nput]1 In1 (NULL )] :Essential :Input:PDB
- [-i[nput]2 In2 (NULL )] :Essential :Input:PDB
- [-o[utput] Out (NULL )] :Essential :Output:PDB
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput]1 In1 (NULL ).as(inFile ) ] :Essential :Input:PDB
+ [-i[nput]2 In2 (NULL ).as(inFile ) ] :Essential :Input:PDB
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output:PDB
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
In2 is a subgroup of In1.
</PRE>
-/bin/bash: pdbCrystalCreate: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbCrystalCreate</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbCrystalCreate</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbCrystalCreate
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input:PDB
+ [-I[nfo] Info (NULL ).as(inFile ) ] :Essential :Input:Crystal Information
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output:PDB
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+----- CrystalInfo -----
+aAxis %15.6g %15.6g %15.6g
+bAxis %15.6g %15.6g %15.6g
+cAxis %15.6g %15.6g %15.6g
+CellLength %15.6g %15.6g %15.6g
+Origin %15.6g %15.6g %15.6g
+N %15d %15d %15d
+StartN %15d %15d %15d
+SpaceGroup %15d
+HelixInfo %10d %10d %10d
+### Attention ###
+Parameter Order is important: Dependent between CellLength and a|b|cAxis.
+ Because each of aAxis, bAxis, cAxis must be a unit vector.
+HelixInfo t u n
+----- CrystalSpaceGroup -----
+ 0 P1
+ 1 HelicalSymmmetry
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: pdbDisplay
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: pdbFileMerge
Options:
- [-i[nput]1 In1 (NULL )] :Essential :InputDataFile
- [-i[nput]2 In2 (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-startC startID (A )] :Optional :start chain ID
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput]1 In1 (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i[nput]2 In2 (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-startC startID (A ).as(Character ) ] :Optional :start chain ID
+ [-NCC[NotChangingChainID] ] :Optional :NotChangingChainID
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
-/bin/bash: pdbHelix: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbHelix</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbHelix</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbHelix
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-3[D] Out3D (NULL ).as(outFile ) ] :Optional :OutputDataFile(3D-mrc)
+ [-2[D] Out2D (NULL ).as(outFile ) ] :Optional :OutputDataFile(2D-mrc projection(y-z))
+ [-d[elta] delta (5 ).as(Real ) ] :Optional :delta[A](mrc-file)
+ [-p[delphi] delphi (165 ).as(Real ) ] :Essential :deltaPhi
+ [-dp[delphi] deldelphi (5 ).as(Real ) ] :Optional :deltaDeltaPhi
+ [-z[deltaz] delz (5 ).as(Real ) ] :Essential :deltaz
+ [-n[Molecule] nMolecule (1 ).as(Integer ) ] :Essential :NumberOfMolecules
+ [-nx nx (1 ).as(Integer ) ] :Optional :Pixel[Def:]
+ [-ny ny (1 ).as(Integer ) ] :Optional :Pixel[Def:]
+ [-nz nz (1 ).as(Integer ) ] :Optional :Pixel[Def:]
+ [-Sx[tart] Startx (0.0 ).as(Real ) ] :Optional :Startx[A]
+ [-Sy[tart] Starty (0.0 ).as(Real ) ] :Optional :Starty[A]
+ [-Sz[tart] Startz (0.0 ).as(Real ) ] :Optional :Startz[A]
+ [-w[eight] Weight (1.0 ).as(Real ) ] :Optional :Weight
+ [-dx dx (2.5 ).as(Real ) ] :Optional :dx
+ [-dy dy (2.5 ).as(Real ) ] :Optional :dy
+ [-dz dz (2.5 ).as(Real ) ] :Optional :dz
+ [-startn startn (0 ).as(Integer ) ] :Optional :start molecule's index
+ [-startC startID (A ).as(Character ) ] :Optional :start chain ID
+ [-deltaSeq deltaSeq (1000 ).as(Integer ) ] :Optional :start chain ID
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: pdbInfo
Options:
- [-i[nput] In (stdin )] :Essential :InputDataFile
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-o[utputWith]a[ppend]OutAppend (stdout )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (stdin ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-o[utputWith]a[ppend]OutAppend (stdout ).as(appendFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: pdbListRMSDCalc
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-r[ef] Ref (NULL )] :Optional :ReferenceDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFileList ) ] :Essential :InputDataFile
+ [-r[ef] Ref (NULL ).as(inFile ) ] :Optional :ReferenceDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
>> -m
0: -i only : against average
-/bin/bash: pdbListVectorCalc: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbListVectorCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbListVectorCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbListVectorCalc
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: pdbMolecularInterfaceFind
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Optional :OutputDataFile
- [-id1[] ID1 (A )] :Optional :ChainId1
- [-id2[] ID2 (B )] :Optional :ChainId2
- [-d[istance] d (1 )] :Optional :Threshold distance
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-id1[] ID1 (A ).as(Character ) ] :Optional :ChainId1
+ [-id2[] ID2 (B ).as(Character ) ] :Optional :ChainId2
+ [-d[istance] d (1 ).as(Real ) ] :Optional :Threshold distance
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
-/bin/bash: pdbMove: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbMove</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbMove</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbMove
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-x X (0.0 ).as(Real ) ] :Optional :Move X[A]
+ [-y Y (0.0 ).as(Real ) ] :Optional :Move Y[A]
+ [-z Z (0.0 ).as(Real ) ] :Optional :Move Z[A]
+ [-originTo toX (0.0 ).as(Real )
+ toY (0.0 ).as(Real )
+ toZ (0.0 ).as(Real ) ] :Optional :move (0,0,0) to (X,Y,Z)
+ [-toOrigin fromX (0.0 ).as(Real )
+ fromY (0.0 ).as(Real )
+ fromZ (0.0 ).as(Real ) ] :Optional :move (X,Y,Z) to (0,0,0)
+ [-GCtoOrigin ] :Optional :GC(Gravity Centre) to origin
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: pdbNAMDRestraintCreate
Options:
- [-i[nput] In (NULL )] :Essential :Input:PDB
- [-r[efrence] Ref (NULL )] :Essential :Input:PDB
- [-o[utput] Out (stdout )] :Optional :Output: NAMD Restraint
- [-O[utput] Out2 (stdout )] :Optional :Output: NAMD PDB Force
- [-kf Kf (1.0 )] :Optional :Input: Kf kcal/mol/A^2
- [-autokf AutoKf (1.0 )] :Optional :Input: Kf kcal/mol for averaged length
- [-seg[name] SegName (EXAMPLE )] :Optional :Input: segment name
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input:PDB
+ [-r[efrence] Ref (NULL ).as(inFile ) ] :Essential :Input:PDB
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: NAMD Restraint
+ [-O[utput] Out2 (stdout ).as(outFile ) ] :Optional :Output: NAMD PDB Force
+ [-kf Kf (1.0 ).as(Real ) ] :Optional :Input: Kf kcal/mol/A^2
+ [-autokf AutoKf (1.0 ).as(Real ) ] :Optional :Input: Kf kcal/mol for averaged length
+ [-seg[name] SegName (EXAMPLE ).as(String ) ] :Optional :Input: segment name
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
-autokf is prior to -kf.
</PRE>
<PRE>
Usage: pdbNearAtomListShow
Options:
- [-i[nput] In (NULL )] :Essential :Input: pdbFile
- [-o[utput] Out (stdout )] :Optional :Output: Coordinates List
- [-P[ointOfInterest] Px (0.0 )Py (0.0 )Pz (0.0 )] :Optional :PointOfInterest: Coordinates
- [-V[olumeOfInterest] MRC (NULL )] :Optional :VolumeOfInterest: MRC
- [-C[outourLevel] Contour (0.0 )] :Optional :ContourLevel for VolumeOfInterest: MRC
- [-d[istance] distance (0.0 )] :Optional :Distance [A]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: pdbFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: Coordinates List
+ [-P[ointOfInterest] Px (0.0 ).as(Real )
+ Py (0.0 ).as(Real )
+ Pz (0.0 ).as(Real ) ] :Optional :PointOfInterest: Coordinates
+ [-V[olumeOfInterest] MRC (NULL ).as(inFile ) ] :Optional :VolumeOfInterest: MRC
+ [-C[outourLevel] Contour (0.0 ).as(Real ) ] :Optional :ContourLevel for VolumeOfInterest: MRC
+ [-d[istance] distance (0.0 ).as(Real ) ] :Optional :Distance [A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: pdbOneProteinGet
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-N[umber] Num (0 )] :Optional :Number[0->]
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-N[umber] Num (0 ).as(Integer ) ] :Optional :Number[0->]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
-/bin/bash: pdbPCA: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbPCA</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbPCA</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbPCA
+Options:
+ [-i[nput] In (stdin ).as(inFile ) ] :Optional :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: Result
+ [-o[utput]U[nit] OutUnit (NULL ).as(outFile ) ] :Optional :Output: Unit Vector Array
+ [-o[utput]M[atrix3D] OutMat3D (NULL ).as(outFile ) ] :Optional :Output: Matrix3D from Unit Vector Array
+ [-o[utput]PDB OutPDB (NULL ).as(outFile ) ] :Optional :Output: PDB rotated from Unit Vector Array
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: pdbProteinIDSet
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-ID ID (A )] :Essential :ChainID
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-ID ID (A ).as(Character ) ] :Essential :ChainID
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
-/bin/bash: pdbRhoFit: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbRhoFit</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbRhoFit</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbRhoFit
+Options:
+ [-i[nput]pdb[File] InPdb (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i[nput]mrc[File] InMrc (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput of ]mrc OutMrc (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-o[utput of ]txt OutTxt (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-o[utput of ]par OutPar (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-o[utput of ]pdb OutPDB (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-xmin xmin (0 ).as(Real ) ] :Optional :xmin for fitting
+ [-xmax xmax (0 ).as(Real ) ] :Optional :xmax for fitting
+ [-xd[elta] xDelta (1 ).as(Real ) ] :Optional :delta x for fitting
+ [-ymin ymin (0 ).as(Real ) ] :Optional :ymin for fitting
+ [-ymax ymax (0 ).as(Real ) ] :Optional :ymax for fitting
+ [-yd[elta] yDelta (1 ).as(Real ) ] :Optional :delta y for fitting
+ [-zmin zmin (0 ).as(Real ) ] :Optional :zmin for fitting
+ [-zmax zmax (82 ).as(Real ) ] :Optional :zmax for fitting
+ [-zd[elta] zDelta (1 ).as(Real ) ] :Optional :delta z for fitting
+ [-E[uler]A[ngle] EulerAngle (ZOYS ).as(String ) ] :Optional :Euler Angle for three-angle
+ [-phimin phimin (0 ).as(Real ) ] :Optional :phimin for fitting(degree)
+ [-phimax phimax (194 ).as(Real ) ] :Optional :phimax for fitting(degree)
+ [-phid[elta] phiDelta (2 ).as(Real ) ] :Optional :delta phi for fitting(degree)
+ [-psimin psimin (0 ).as(Real ) ] :Optional :psimin for fitting(degree)
+ [-psimax psimax (0 ).as(Real ) ] :Optional :psimax for fitting(degree)
+ [-psid[elta] psiDelta (2 ).as(Real ) ] :Optional :delta psi for fitting(degree)
+ [-thetamin thetamin (0 ).as(Real ) ] :Optional :thetamin for fitting(degree)
+ [-thetamax thetamax (0 ).as(Real ) ] :Optional :thetamax for fitting(degree)
+ [-thetad[elta] thetaDelta (2 ).as(Real ) ] :Optional :delta theta for fitting(degree)
+ [-n[ormalize]w[eight]normalizeWeight (100000000.0).as(Real ) ] :Optional :weight for normalize
+ [-n[ormalize]C[ontour]normalizeContour (0.0 ).as(Real ) ] :Optional :Contour Level for Normalize
+ [-I[nverse] ] :Optional :Black is High Density.
+ [-Zminus ] :Optional :Shift to -z
+ [-Tfactor ] :Optional :Consider T factor
+ [-T[ factor ]lim[it] Tlim (60 ).as(Real ) ] :Optional :The atom will be neglected
+ [-Centre ] :Optional :Filament-axis is x=0, y=0
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-C[ontour] contourLevel (0.0 ).as(Real ) ... ] :Variable :ContourLevel
+
+
+Usage of pdbRhoFit:
+ -ipdb : Filename of pdb file of atomic model
+ -imrc : Filename of mrc file of contour map
+ -omrc : Filename of mrc file of fitting results
+ -otxt : Filename of text file of fitting results
+ -opar : Filename of text file of fitting results
+ -opdb : Filename of pdb file with a max score after fitting results
+ -zmin : Initial value of z (should <= zmax)
+ -zmax : Final value of z
+ -zd : Delta z for fitting (should >0)
+ -phimin : Initial value of phi (should <= phimax; initial value of phi is 0)
+ -phimax : Final value of phi (should >0)
+ -phid : Delta phi for fitting (should >0)
+ -C : Contour level (variable and MUST be last option)
+ -Inverse: Protein has high density on the image
+ -Zminus : Atomic model shift to -z while fitting
+ -Tfactor: Consider temperature factor
+ -Tlim : The atoms whose T factor is above Tlim will be neglected
+ -Centre : Filament-axis is x=0, y=0
+ -c : Not used now
+ -m 0 : Count the atom number inside the contour.
+ 1 : Add the densities of atoms.
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbRhoFitCoiledCoil: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbRhoFitCoiledCoil</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbRhoFitCoiledCoil</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbRhoFitCoiledCoil
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbRhoFitTm: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbRhoFitTm</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbRhoFitTm</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbRhoFitTm
+Options:
+ [-i[nput]pdb[File] InPdb (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i[nput]mrc[File] InMrc (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput of ]mrc OutMrc (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-Sx Sx (50 ).as(Real ) ] :Essential :x of rotation axis
+ [-Sy Sy (110 ).as(Real ) ] :Essential :y of rotation axis
+ [-Sz Sz (110 ).as(Real ) ] :Essential :z of rotation axis
+ [-o[utput of ]txt OutTxt (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-o[utput of ]pdb OutPDB (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-xmin xmin (0 ).as(Real ) ] :Optional :xmin for fitting
+ [-xmax xmax (0 ).as(Real ) ] :Optional :xmax for fitting
+ [-xd[elta] xDelta (1 ).as(Real ) ] :Optional :delta x for fitting
+ [-ymin ymin (0 ).as(Real ) ] :Optional :ymin for fitting
+ [-ymax ymax (0 ).as(Real ) ] :Optional :ymax for fitting
+ [-yd[elta] yDelta (1 ).as(Real ) ] :Optional :delta y for fitting
+ [-zmin zmin (0 ).as(Real ) ] :Optional :zmin for fitting
+ [-zmax zmax (82 ).as(Real ) ] :Optional :zmax for fitting
+ [-zd[elta] zDelta (1 ).as(Real ) ] :Optional :delta z for fitting
+ [-E[uler]A[ngle] EulerAngle (ZOYS ).as(String ) ] :Optional :Euler Angle for three-angle
+ [-phimin phimin (0 ).as(Real ) ] :Optional :phimin for fitting(degree)
+ [-phimax phimax (194 ).as(Real ) ] :Optional :phimax for fitting(degree)
+ [-phid[elta] phiDelta (2 ).as(Real ) ] :Optional :delta phi for fitting(degree)
+ [-psimin psimin (0 ).as(Real ) ] :Optional :psimin for fitting(degree)
+ [-psimax psimax (0 ).as(Real ) ] :Optional :psimax for fitting(degree)
+ [-psid[elta] psiDelta (2 ).as(Real ) ] :Optional :delta psi for fitting(degree)
+ [-thetamin thetamin (0 ).as(Real ) ] :Optional :thetamin for fitting(degree)
+ [-thetamax thetamax (0 ).as(Real ) ] :Optional :thetamax for fitting(degree)
+ [-thetad[elta] thetaDelta (2 ).as(Real ) ] :Optional :delta theta for fitting(degree)
+ [-n[ormalize]w[eight]normalizeWeight (100000000.0).as(Real ) ] :Optional :weight for normalize
+ [-n[ormalize]C[ontour]normalizeContour (0.0 ).as(Real ) ] :Optional :Contour Level for Normalize
+ [-I[nverse] ] :Optional :Black is High Density.
+ [-Zminus ] :Optional :Shift to -z
+ [-Tfactor ] :Optional :Consider T factor
+ [-T[ factor ]lim[it] Tlim (60 ).as(Real ) ] :Optional :The atom will be neglected
+ [-Centre ] :Optional :Filament-axis is x=0, y=0
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-C[ontour] contourLevel (0.0 ).as(Real ) ... ] :Variable :ContourLevel
+
+
+Usage of pdbRhoFitTm:
+ -ipdb : Filename of pdb file of atomic model
+ -imrc : Filename of mrc file of contour map
+ -omrc : Filename of mrc file of fitting results
+ -otxt : Filename of text file of fitting results
+ -opdb : Filename of pdb file with a max score after fitting results
+ -zmin : Initial value of z (should <= zmax)
+ -zmax : Final value of z
+ -zd : Delta z for fitting (should >0)
+ -phimin : Initial value of phi (should <= phimax; initial value of phi is 0)
+ -phimax : Final value of phi (should >0)
+ -phid : Delta phi for fitting (should >0)
+ -C : Contour level (variable and MUST be last option)
+ -Inverse: Protein has high density on the image
+ -Sx : x of rotation axis
+ -Sy : y of rotation axis
+ -Sz : z of rotation axis
+ -Zminus : Atomic model shift to -z while fitting
+ -Tfactor: Consider temperature factor
+ -Tlim : The atoms whose T factor is above Tlim will be neglected
+ -Centre : Filament-axis is x=0, y=0
+ -c : Not used now
+ -m 0 : Count the atom number inside the contour.
+ 1 : Add the densities of atoms.
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbRotation: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbRotation</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbRotation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbRotation
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-ZXY ZXYrotx (0.0 ).as(Real )
+ ZXYroty (0.0 ).as(Real )
+ ZXYrotz (0.0 ).as(Real ) ] :Optional :ZXY*pdb: rotz(rotz)rotx(rotx)roty(roty)
+ [-ZYX ZYXrotx (0.0 ).as(Real )
+ ZYXroty (0.0 ).as(Real )
+ ZYXrotz (0.0 ).as(Real ) ] :Optional :ZYX*pdb: rotz(rotz)roty(roty)rotx(rotx)
+ [-YXZ YXZrotx (0.0 ).as(Real )
+ YXZroty (0.0 ).as(Real )
+ YXZrotz (0.0 ).as(Real ) ] :Optional :YXZ*pdb: roty(roty)rotx(rotx)rotz(rotz)
+ [-XYZ XYZrotx (0.0 ).as(Real )
+ XYZroty (0.0 ).as(Real )
+ XYZrotz (0.0 ).as(Real ) ] :Optional :XYZ*pdb: rotx(rotx)roty(roty)rotz(rotz)
+ [-E[uler]A[ngle] RotMode (YOYS ).as(String )
+ Rot1 (0.0 ).as(Real )
+ Rot2 (0.0 ).as(Real )
+ Rot3 (0.0 ).as(Real ) ] :Optional :EA*pdb: EA=rot(rot3)rot(rot2)rot(rot1)
+ [-cuda cudaDeviceID (0 ).as(Integer ) ] :Optional :UseCuda
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+
+ZXY : y-axis -> x-axis -> z->axis
+ZYX : x-axis -> y-axis -> z->axis
+ZXY -> ZYX -> XYZ ->YXZ -> EU
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: pdbSecondaryStructurePrint
Options:
- [-i[nput] In (stdin )] :Optional :Input: pdb
- [-o[utput] Out (stdout )] :Optional :Output: pdb
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (stdin ).as(inFile ) ] :Optional :Input: pdb
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: pdb
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
-/bin/bash: pdbShapeFit: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbShapeFit</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbShapeFit</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbShapeFit
+Options:
+ [-i[nput]pdb[File] InPDB (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i[nput]mrc[File] InMRC (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-C[ontour] Contour (0.0 ).as(Real ) ] :Essential :Contour
+ [-C[ontour]M[ode] ContourMode (0 ).as(Integer ) ] :Optional :ContourMode: refer to mrcImageContourSurfaceCreate
+ [-o[utput of ]mrc OutMRC (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-o[utput of ]txt OutTxt (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-o[utput of ]pdb OutPDB (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-xmin xmin (0 ).as(Real ) ] :Optional :xmin for fitting
+ [-xmax xmax (0 ).as(Real ) ] :Optional :xmax for fitting
+ [-xd[elta] xDelta (1 ).as(Real ) ] :Optional :delta x for fitting
+ [-ymin ymin (0 ).as(Real ) ] :Optional :ymin for fitting
+ [-ymax ymax (0 ).as(Real ) ] :Optional :ymax for fitting
+ [-yd[elta] yDelta (1 ).as(Real ) ] :Optional :delta y for fitting
+ [-zmin zmin (0 ).as(Real ) ] :Optional :zmin for fitting
+ [-zmax zmax (82 ).as(Real ) ] :Optional :zmax for fitting
+ [-zd[elta] zDelta (1 ).as(Real ) ] :Optional :delta z for fitting
+ [-E[uler]A[ngle] EulerAngle (ZOYS ).as(String ) ] :Optional :Euler Angle for three-angle
+ [-phimin phimin (0 ).as(Real ) ] :Optional :phimin for fitting(degree)
+ [-phimax phimax (194 ).as(Real ) ] :Optional :phimax for fitting(degree)
+ [-phid[elta] phiDelta (2 ).as(Real ) ] :Optional :delta phi for fitting(degree)
+ [-psimin psimin (0 ).as(Real ) ] :Optional :psimin for fitting(degree)
+ [-psimax psimax (0 ).as(Real ) ] :Optional :psimax for fitting(degree)
+ [-psid[elta] psiDelta (2 ).as(Real ) ] :Optional :delta psi for fitting(degree)
+ [-thetamin thetamin (0 ).as(Real ) ] :Optional :thetamin for fitting(degree)
+ [-thetamax thetamax (0 ).as(Real ) ] :Optional :thetamax for fitting(degree)
+ [-thetad[elta] thetaDelta (2 ).as(Real ) ] :Optional :delta theta for fitting(degree)
+ [-P[DB]C[ontour]M[ode]surfaceMode (0 ).as(Integer ) ] :Optional :PDB SurfaceMode: refer to pdbSurface
+ [-order order (1.7 ).as(Real ) ] :Optional :order: refer to pdbSurface
+ [-refine refine (2 ).as(Integer ) ] :Optional :refine: refer to pdbSurface
+ [-size size (3 ).as(Integer ) ] :Optional :size: refer to pdbSurface
+ [-weight weight (100 ).as(Real ) ] :Optional :weight: refer to pdbSurface
+ [-mergin mergin (3.0 ).as(Real ) ] :Optional :mergin: refer to pdbSurface
+ [-thres thresHold (0.0 ).as(Real ) ] :Optional :threshold: refer to pdbSurface
+ [-I[nverse] ] :Optional :Black is High Density.
+ [-Centre ] :Optional :Filament-axis is x=0, y=0
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+ -ipdb : Filename : An atomic model to be fitted (PDB)
+ -imrc : Filename : 3-D density map (mrc-formated)
+ -omrc : Filename : fitting score map (MRC)
+ z=0: a max-score map of an phi-z plane which includes a max score point.
+ The max score mean a maximum score in all x-y-psi-theta plane with specific values of phi and z.
+ z=1: a max-score map of an psi-theta plane which includes a max score point.
+ The max score mean a maximum score in all x-y plane with specific values of psi, theta, phi and z.
+ z=2: a score map of an x-y plane which includes a max score point.
+ -otxt : Filename : fitting results (Text)
+ -opdb : Filename : An atomic model with a maximum score after fitting
+ -x|y|zmin : Initial value of z (should <= zmax)
+ -x|y|zmax : Final value of z
+ -x|y|zd : Delta z for fitting (should !=0)
+ -phi|psi|thetamin : Initial value of phi (should <= phimax; initial value of phi is 0)
+ -phi|psi|thetamax : Final value of phi (should !=0)
+ -phi|psi|thetad : Delta phi for fitting (should >0)
+ -C : Contour level of map file
+ -Inverse: Protein has high density on the image
+ -Centre : Filament-axis in an inPDBFile is along the line of x=0, y=0
+ -EA : Euler Angle Set : ZOYS: z -> y -> x
+ -c : Not used now
+ -m 0 : Count the atom number inside the contour.
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: pdbSurface
Options:
- [-i[nput] In (NULL )] :Essential :Input: pdbFile
- [-o[utput] Out (NULL )] :Essential :Output: pdbFile
- [-order order (1.7 )] :Optional :Order: [A]
- [-refine refine (2 )] :Optional :Refine: Meshsize = Order/Refine
- [-size size (3 )] :Optional :Refine: Shell thickness = Order/Refine*Size
- [-weight weight (100.0 )] :Optional :Weight
- [-mergin mergin (3.0 )] :Optional :SearchArea
- [-thres thresHold (0.0 )] :Optional :thresHold
- [-densityMode DensityMode (0 )] :Optional :DensityMode
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: pdbFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: pdbFile
+ [-order order (1.7 ).as(Real ) ] :Optional :Order: [A]
+ [-refine refine (2 ).as(Integer ) ] :Optional :Refine: Meshsize = Order/Refine
+ [-size size (3 ).as(Integer ) ] :Optional :Refine: Shell thickness = Order/Refine*Size
+ [-weight weight (100.0 ).as(Real ) ] :Optional :Weight
+ [-mergin mergin (3.0 ).as(Real ) ] :Optional :SearchArea
+ [-thres thresHold (0.0 ).as(Real ) ] :Optional :thresHold
+ [-densityMode DensityMode (0 ).as(Integer ) ] :Optional :DensityMode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: pdbTempFactorSet
Options:
- [-i[nput] In (NULL )] :Essential :Input: pdbFile
- [-r[eference] Ref (stdin )] :Optional :Input: selectionFile
- [-o[utput] Out (NULL )] :Essential :Output: pdbFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: pdbFile
+ [-r[eference] Ref (stdin ).as(inFile ) ] :Optional :Input: selectionFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: pdbFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
-/bin/bash: pdbTrans: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbTrans</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbTrans</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbTrans
+Options:
+ [-i[nput] inFile (NULL ).as(inFile ) ] :Essential :Input: DataFile
+ [-o[utput] outFile (NULL ).as(outFile ) ] :Essential :Output: DataFile
+ [-M[atrix] matFile (NULL ).as(inFile ) ] :Optional :Input: MatrixFile[4][4]
+ [-E[uler]A[ngle] RotMode (YOYS ).as(String )
+ Rot1 (0.0 ).as(Real )
+ Rot2 (0.0 ).as(Real )
+ Rot3 (0.0 ).as(Real ) ] :Optional :Input:
+ [-cuda cudaDeviceID (0 ).as(Integer ) ] :Optional :cuda
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+>>> Matrix3D File Format y = Ax + b<<<
+a11 a21 a31 : Rotation Array : y=Ax
+a12 a22 a32
+a13 a23 a33
+b1 b2 b3 : Translation Array : y = x + b
+--- Attention ---
+If both options of -M and -EA are set,
+ first, translation and rotation by -M will be performed
+ then, rotation by -EA will be done.
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbTwoProteinFit: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbTwoProteinFit</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbTwoProteinFit</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbTwoProteinFit
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i[nput]res[idue] InResidue (NULL ).as(inFile ) ] :Optional :ResidueInformationOfInputData
+ [-i[nput]sel[ectResidue]SelectIn (NULL ).as(outFile ) ] :Optional :Output: Selected residue of in after fitting
+ [-r[ef] Ref (NULL ).as(inFile ) ] :Essential :ReferenceDataFile
+ [-r[ef]res[idue] RefResidue (NULL ).as(inFile ) ] :Optional :ResidueInfomationOfReferenceData
+ [-r[ef]sel[ectResidue]SelectRef (NULL ).as(outFile ) ] :Optional :Output: Selected residue of after fitting
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-o[utput]Matrix Matrix (stdout ).as(outFile ) ] :Optional :OutputMatrix
+ [-o[utput]Param Param (stdout ).as(outFile ) ] :Optional :OutputParam
+ [-o[utput]Dis[tance] outDis (stdout ).as(outFile ) ] :Optional :Output: PDB Distance as Temp
+ [-o[utput]Dis[tance]2outDis2 (stdout ).as(outFile ) ] :Optional :Output: Distance List for Ca
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+>>>> Input and Reference File Format<<<<
+ResidueNumberToBeFitted
+...
+If |, all residules are sellected till the residue in the next line
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: pdbWaterAdd
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-d[ensity] Density (55.55555 )] :Optional :[M]: Density of Water
- [-r[adius] Radius (100. )] :Optional :[A]: Radius of Water Volume: Sphere, Cylinder
- [-height Height (100. )] :Optional :[A]: Height of Water Volume : Cylinder
- [-cube X (100. )Y (100. )Z (100. )] :Optional :[A]: Cube
- [-edge Edge (3. )] :Optional :layer number: Edge
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-d[ensity] Density (55.55555 ).as(Real ) ] :Optional :[M]: Density of Water
+ [-r[adius] Radius (100. ).as(Real ) ] :Optional :[A]: Radius of Water Volume: Sphere, Cylinder
+ [-height Height (100. ).as(Real ) ] :Optional :[A]: Height of Water Volume : Cylinder
+ [-cube X (100. ).as(Real )
+ Y (100. ).as(Real )
+ Z (100. ).as(Real ) ] :Optional :[A]: Cube
+ [-edge Edge (3. ).as(Integer ) ] :Optional :layer number: Edge
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- Mode: -m -----
-m 0 : sphere
<PRE>
Usage: pointAffineTransform
Options:
- [-p[oint] X (0 )Y (0 )Z (0 )] :Essential :Input: Points
- [-Euler Euler (YOYS )Rot1 (0 )Rot2 (0 )Rot3 (0 )] :Optional :Input: EuerAngle
- [-shift dX (0 )dY (0 )dZ (0 )] :Optional :Input: shift[pixel]
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-p[oint] X (0 ).as(Real )
+ Y (0 ).as(Real )
+ Z (0 ).as(Real ) ] :Essential :Input: Points
+ [-Euler Euler (YOYS ).as(String )
+ Rot1 (0 ).as(Real )
+ Rot2 (0 ).as(Real )
+ Rot3 (0 ).as(Real ) ] :Optional :Input: EuerAngle
+ [-shift dX (0 ).as(Real )
+ dY (0 ).as(Real )
+ dZ (0 ).as(Real ) ] :Optional :Input: shift[pixel]
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
-/bin/bash: pointsSetToPDB: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pointsSetToPDB</TITLE>
+</HEAD>
+<BODY>
+<H1>pointsSetToPDB</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pointsSetToPDB
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: PointsSet
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: PDB
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>probabilityDensityFunction</TITLE>
+</HEAD>
+<BODY>
+<H1>probabilityDensityFunction</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: probabilityDensityFunction
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: psFileMerge
Options:
- [-i[nput file]1 In1 (NULL )] :Essential :InputDataFile1
- [-i[nput file]2 In2 (NULL )] :Essential :InputDataFile2
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput file]1 In1 (NULL ).as(inFile ) ] :Essential :InputDataFile1
+ [-i[nput file]2 In2 (NULL ).as(inFile ) ] :Essential :InputDataFile2
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: psFilePageMerge
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-p[age] Page (2 )] :Optional :PageNumberToBeMerged
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-p[age] Page (2 ).as(Integer ) ] :Optional :PageNumberToBeMerged
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: randomNormalGet
Options:
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-O[utput] OutMRC (NULL )] :Optional :OutputDataFile(mrcImage)
- [-n N (100 )] :Optional :number
- [-a[verage] Ave (0.0 )] :Optional :average
- [-sd SD (1.0 )] :Optional :SD
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-O[utput] OutMRC (NULL ).as(outFile ) ] :Optional :OutputDataFile(mrcImage)
+ [-n N (100 ).as(Integer ) ] :Optional :number
+ [-a[verage] Ave (0.0 ).as(Real ) ] :Optional :average
+ [-sd SD (1.0 ).as(Real ) ] :Optional :SD
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: randomUniformGet
Options:
- [-o[utput] Out (stdout )] :Optional :OutputDataFile
- [-min min (0.0 )] :Optional :Minimum of Number
- [-max max (1.0 )] :Optional :Maximum of Number
- [-n[umber] num (1 )] :Optional :Number
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-min min (0.0 ).as(Real ) ] :Optional :Minimum of Number
+ [-max max (1.0 ).as(Real ) ] :Optional :Maximum of Number
+ [-n[umber] num (1 ).as(Integer ) ] :Optional :Number
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
</PRE>
</BODY>
</HTML>
<PRE>
Usage: rasmonyo
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: tgaInfo
Options:
- [-i[nput] In (stdin )] :Optional :Input: tgaFile or Pipe
- [-o[utput] Out (stdout )] :Optional :Output: ASCII
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] In (stdin ).as(inFile ) ] :Optional :Input: tgaFile or Pipe
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: ASCII
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: tiff2mrc
Options:
- [-i[nput] inFile (NULL )] :Essential :InputDataFile
- [-o[utput] outFile (NULL )] :Essential :OutputDataFile
- [-r[esolution] Resolution (2.5 )] :Optional :Resolution[A]
- [-t[ime] time (1.0 )] :Optional :x OptimalTime
- [-d[irnum] dirnum (0 )] :Optional :tiffDirectoryNumber
- [-I[nverse] ] :Optional :Black<->White
- [-Signed ] :Optional :Original image is Signed or Not: Default unsigned
- [-Offset Offset (0.0 )] :Optional :OffsetValue
- [-Max Max (16 )] :Optional :MaxValue:2^Max
- [-Min Min (1 )] :Optional :MinValue:2^Min: without 0
- [-realMin realMin (0.0 )] :Optional :Real MinValue
- [-realMax realMax (0.0 )] :Optional :Real MaxValue
- [-realMaxBit realMaxBit (14 )] :Optional :Real MaxValue Bit
- [-sin sinFile (NULL )] :Optional :sin file from Zeiss
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-S[hrink] Shrink (8 )] :Optional :ShrinkMode
- [-M[ode] Mode (0 )] :Optional :Mode: mrcMode: Def: if -m 0, -M 0. if -m 1 -M 2
- [-m[ode] mode (0 )] :Optional :Mode: 0 (Direct), 1(Log10(65535/data))
+ [-i[nput] inFile (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] outFile (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-r[esolution] Resolution (2.5 ).as(Real ) ] :Optional :Resolution[A]
+ [-t[ime] time (1.0 ).as(Real ) ] :Optional :x OptimalTime
+ [-d[irnum] dirnum (0 ).as(Integer ) ] :Optional :tiffDirectoryNumber
+ [-I[nverse] ] :Optional :Black<->White
+ [-Signed ] :Optional :Original image is Signed or Not: Default unsigned
+ [-Offset Offset (0.0 ).as(Real ) ] :Optional :OffsetValue
+ [-Max Max (16 ).as(Real ) ] :Optional :MaxValue:2^Max
+ [-Min Min (1 ).as(Real ) ] :Optional :MinValue:2^Min: without 0
+ [-realMin realMin (0.0 ).as(Real ) ] :Optional :Real MinValue
+ [-realMax realMax (0.0 ).as(Real ) ] :Optional :Real MaxValue
+ [-realMaxBit realMaxBit (14 ).as(Real ) ] :Optional :Real MaxValue Bit
+ [-sin sinFile (NULL ).as(inFile ) ] :Optional :sin file from Zeiss
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-S[hrink] Shrink (8 ).as(Integer ) ] :Optional :ShrinkMode
+ [-M[ode] Mode (0 ).as(Integer ) ] :Optional :Mode: mrcMode: Def: if -m 0, -M 0. if -m 1 -M 2
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode: 0 (Direct), 1(Log10(65535/data))
---- mode ----
0x0000000f bits: Direct or Log
0x000000f0 bits: Which Color
<PRE>
Usage: tiltInfoDetermine
Options:
- [-i[nput] In (NULL )] :Essential :InputDataFile
- [-defocusIn[put] defocus (NULL )] :Essential :InputDataFile
- [-o[utput] Out (NULL )] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
- [-M[ag] mag (2.4 )] :Optional :Mag
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-defocusIn[put] defocus (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-M[ag] mag (2.4 ).as(Real ) ] :Optional :Mag
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: vector2pdb
Options:
- [-v[ector] vx (1 )vy (0 )vz (0 )] :Optional :Input: vector
- [-polar[vector] phi (0 )theta (0 )] :Optional :Input: vector[degree]
- [-polarz[axis] zx (0 )zy (0 )zz (1 )] :Optional :Input: z-axis for polar
- [-polarx[axis] xx (1 )xy (0 )xz (0 )] :Optional :Input: x-axis for polar
- [-ori[ginal] sx (0 )sy (3 )sz (0 )] :Optional :Input: origin
- [-step step (1.6 )] :Optional :Input: step [A]
- [-o[utput] Out (stdout )] :Optional :Output: pdbFile
- [-n n (20 )] :Optional :Input: Number Of CA
- [-ID ID (A )] :Optional :Input: Chain ID
- [-Res Res (GLY )] :Optional :Input: Chain ID
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-v[ector] vx (1 ).as(Real )
+ vy (0 ).as(Real )
+ vz (0 ).as(Real ) ] :Optional :Input: vector
+ [-polar[vector] phi (0 ).as(Real )
+ theta (0 ).as(Real ) ] :Optional :Input: vector[degree]
+ [-polarz[axis] zx (0 ).as(Real )
+ zy (0 ).as(Real )
+ zz (1 ).as(Real ) ] :Optional :Input: z-axis for polar
+ [-polarx[axis] xx (1 ).as(Real )
+ xy (0 ).as(Real )
+ xz (0 ).as(Real ) ] :Optional :Input: x-axis for polar
+ [-ori[ginal] sx (0 ).as(Real )
+ sy (3 ).as(Real )
+ sz (0 ).as(Real ) ] :Optional :Input: origin
+ [-step step (1.6 ).as(Real ) ] :Optional :Input: step [A]
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: pdbFile
+ [-n n (20 ).as(Integer ) ] :Optional :Input: Number Of CA
+ [-ID ID (A ).as(Character ) ] :Optional :Input: Chain ID
+ [-Res Res (GLY ).as(String ) ] :Optional :Input: Chain ID
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
<PRE>
Usage: vectorImageNearestNeighborMethod
Options:
- [-i[nput] InList (NULL )] :Essential :Input: filelist
- [-O[utput] Outclassification (NULL )] :Essential :Output: ClassificationDataFile
- [-o[utput]c[lassification]i[ntegration]r[ate]OutClassificationIntegrationRate(NULL )] :Optional :OutputClassificationIntegrationRate: classificationIntegrationRatefile
- [-o[utput]d[istance] OutDistance (NULL )] :Optional :OutputDistance: distancefile
- [-o[utput]d[istance]r[ate]OutDistanceRate (NULL )] :Optional :OutputDistanceRate: distanceRatefile
- [-o[utput]u[pper]d[istance]n[umberOfClasses]OutUpperDistanceRate(NULL )] :Optional :OutputUpperDistanceNumberOfClasses: upperDistanceRatefile
- [-o[utput]u[pper]d[istance]c[lassificationDatafile]OutClassName (NULL )] :Optional :OutputUpperDistanceClassificationDatafile: ClassificationDatafile
- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
- [-m[ode] mode (0 )] :Optional :Mode
+ [-i[nput] InList (NULL ).as(inFileListNoOpen ) ] :Essential :Input: filelist
+ [-O[utput] Outclassification (NULL ).as(outFile ) ] :Essential :Output: ClassificationDataFile
+ [-o[utput]c[lassification]i[ntegration]r[ate]OutClassificationIntegrationRate(NULL ).as(outFile ) ] :Optional :OutputClassificationIntegrationRate: classificationIntegrationRatefile
+ [-o[utput]d[istance] OutDistance (NULL ).as(outFile ) ] :Optional :OutputDistance: distancefile
+ [-o[utput]d[istance]r[ate]OutDistanceRate (NULL ).as(outFile ) ] :Optional :OutputDistanceRate: distanceRatefile
+ [-o[utput]u[pper]d[istance]n[umberOfClasses]OutUpperDistanceRate(NULL ).as(outFile ) ] :Optional :OutputUpperDistanceNumberOfClasses: upperDistanceRatefile
+ [-o[utput]u[pper]d[istance]c[lassificationDatafile]OutClassName (NULL ).as(outFile ) ] :Optional :OutputUpperDistanceClassificationDatafile: ClassificationDatafile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
</PRE>
</BODY>
OSDN Git Service
