<H2>Information from source codes</H2>
</A>
<PRE>
-../src/contourCreate.c:
-
-../src/lcontour2ps.c:
-
-../src/lmrc2contour.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/tkImgFmtMRC.c:
-
-../src/tkImgFmtlargeIP.c:
-
-../src/tkctfInfo.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/avsFileInit.c:
-
-../src/avsFileSet.c:
-
-../src/avsFileWrite.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/density_sphere.c:
-
-../src/drawWireFrame.c:
-
-../src/lmolvieCamera.c:
-
-../src/lmolvieDisplayLib.c:
-
-../src/lmolvieDisplayListMake.c:
-
-../src/lmolvieDisplayNormal.c:
-
-../src/lmolvieDisplayParallel.c:
-
-../src/lmolvieDockDisplay.c:
-
-../src/lmolvieDockKeyboard.c:
-
-../src/lmolvieFlightDisplay.c:
-
-../src/lmolvieFlightIdle.c:
-
-../src/lmolvieFlightKeyboard.c:
-
-../src/lmolvieIdleNormal.c:
-
-../src/lmolvieInitNormal.c:
-
-../src/lmolvieInitParallel.c:
-
-../src/lmolvieKeyboard.c:
-
-../src/lmolvieKeyboardDrive.c:
-
-../src/lmolvieKeyboardMulti.c:
-
-../src/lmolvieKeyboardNormal.c:
-
-../src/lmolvieKeyboardParallel.c:
-
-../src/lmolvieKeyboardSurface.c:
-
-../src/lmolvieLight.c:
-
-../src/lmolvieMRCread.c:
-
-../src/lmolvieMouse.c:
-
-../src/lmolvieMouseDrive.c:
-
-../src/lmolvieMouseMulti.c:
-
-../src/lmolvieMouseNormal.c:
-
-../src/lmolvieMouseParallel.c:
-
-../src/lmolvieMrcViewerDisplay.c:
-
-../src/lmolvieMrcViewerKeyboard.c:
-
-../src/lmolvieMrcViewerMouse.c:
-
-../src/lmolvieOperation.c:
-
-../src/lmolviePDBread.c:
-
-../src/lmolvieProjectionKeyboard.c:
-
-../src/lmolvieProjectionMouse.c:
-
-../src/lmolvieProteinStatus.c:
-
-../src/lmolvieReshapeNormal.c:
-
-../src/lmolvieReshapeParallel.c:
-
-../src/lmolvieTest.c:
-
-../src/lmolvieTexture.c:
-
-../src/lmolvieViewerDisplay.c:
-
-../src/lmolvieViewerIdle.c:
-
-../src/lmolvieViewerKeyboard.c:
-
-../src/lmolvieViewerMouse.c:
-
-../src/lmolvieViewerSpecial.c:
-
-../src/lmolvieVoice.c:
-
-../src/loadPDB.c:
-
-../src/loadPPM.c:
-
-../src/marching_cubes.c:
-
-../src/multiPDB.c:
-
-../src/openGLKey.c:
-
-../src/savePPM.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/decoder.c:
-
-../src/gifFileInit.c:
-
-../src/gifFileWrite.c:
-
-../src/gifUtil.c:
-
-../src/gifcompr.c:
-
-../src/gifencod.c:
-
-../src/lmrc2gif.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/lmrc2png.c:
-
-../src/pngFileInit.c:
-
-../src/pngFileWrite.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/psFileCircle.c:
-
-../src/psFileContour.c:
-
-../src/psFileContour3D.c:
-
-../src/psFileEnd.c:
-
-../src/psFileImage.c:
-
-../src/psFileInit.c:
-
-../src/psFileLine.c:
-
-../src/psFilePage.c:
-
-../src/psFileRead.c:
-
-../src/psFileString.c:
-
-../src/psFileUtil.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/lmrc2bild.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/bmpFileInfo.c:
-
-../src/bmpFileRead.c:
-
-../src/lbmp2mrc.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/ctfDeterminationFromPhaseComparison.c:
-
-../src/ctfFunction.c:
-
-../src/ctfInfoPVM.c:
-
-../src/ctfInfoRead.c:
-
-../src/ctfInfoWrite.c:
-
-../src/ctfInfoWrite2.c:
-
-../src/ctfWeight.c:
-
-../src/ctfZeroPoint.c:
-
-../src/ctfforbayes.c:
-
-../src/ctfforbayescheck.c:
-
-../src/defocuslikelihood.c:
-
-../src/lastigmatismDetection.c:
-
-../src/lctfDetermination.c:
-
-../src/lctfDetermine.c:
-
-../src/lmolecularEnvelope.c:
-
-../src/lmrcFSInfoScatteringAngularDistributionAverageSection.c:
-
-../src/powerspectraTangentLine.c:
-
-../src/thonRing.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/dmFileInfo.c:
-
-../src/dmFileInit.c:
-
-../src/dmFileRead.c:
-
-../src/dmFileUtil.c:
-
-../src/ldm2mrc.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/dsn6Init.c:
-
-../src/dsn6Write.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/emDataRead.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/lmrc2viff.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/largeIPRead.c:
-
-../src/tkImgFmtlargeIP.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/llDataCheck.c:
-
-../src/llDataETC.c:
-
-../src/llDataError.c:
-
-../src/llDataGet.c:
-
-../src/llDataInfo.c:
-
-../src/llDataInit.c:
-
-../src/llDataIntensityInformationGet.c:
-
-../src/llDataPVM.c:
-
-../src/llDataRead.c:
-
-../src/llDataSet.c:
-
-../src/llDataUtil.c:
-
-../src/llDataWrite.c:
-
-../src/lll2ltlg.c:
-
-../src/lllDataAdd.c:
-
-../src/lllDataAverage.c:
-
-../src/lllDataAvgTo.c:
-
-../src/lllDataAxisSearch.c:
-
-../src/lllDataAxisSearch2.c:
-
-../src/lllDataAxisSearchAndAverage.c:
-
-../src/lllDataCTFCompensate.c:
-
-../src/lllDataCTFObservation.c:
-
-../src/lllDataCompare.c:
-
-../src/lllDataContributionCalcDifferentN.c:
-
-../src/lllDataDifferenceCalc.c:
-
-../src/lllDataEquatorAdd.c:
-
-../src/lllDataExtract.c:
-
-../src/lllDataFit.c:
-
-../src/lllDataFit2.c:
-
-../src/lllDataFitAndAverage.c:
-
-../src/lllDataFitMergedLL.c:
-
-../src/lllDataFitOut.c:
-
-../src/lllDataFitParamInverse.c:
-
-../src/lllDataFitUtil.c:
-
-../src/lllDataFitUtilPVM.c:
-
-../src/lllDataInterpolate.c:
-
-../src/lllDataLowPassFiltering.c:
-
-../src/lllDataMergeDifferentN.c:
-
-../src/lllDataMultiCTFCompensation.c:
-
-../src/lllDataPhaseShift.c:
-
-../src/lllDataPrint.c:
-
-../src/lllDataRescaling.c:
-
-../src/lllDataSingleCTFCompensation.c:
-
-../src/lllDataWeightSet.c:
-
-../src/lllDatarMaxLimit.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/lltlg2mrc.c:
-
-../src/ltlgDataAllocate.c:
-
-../src/ltlgDataGet.c:
-
-../src/ltlgDataPrint.c:
-
-../src/ltlgDataReadFile.c:
-
-../src/ltlgDataWeightModify.c:
-
-../src/ltlgDataWriteFile.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/mapFileRead.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/fftn.c:
-
-../src/lmrcFETnormalizeBySD.c:
-
-../src/lmrcFFTCentralSection.c:
-
-../src/lmrcFFTCentralSectionCompare.c:
-
-../src/lmrcFFTCentralSectionCompareInfoWrite.c:
-
-../src/lmrcFFTCentralSectionsGet.c:
-
-../src/lmrcFFTExpression.c:
-
-../src/lmrcFFTFGconj.c:
-
-../src/lmrcFFTFxG.c:
-
-../src/lmrcFFTInfo.c:
-
-../src/lmrcImage3DPad.c:
-
-../src/lmrcImage3DWindowing.c:
-
-../src/lmrcImageAddValue.c:
-
-../src/lmrcImageAsProbability.c:
-
-../src/lmrcImageAverage.c:
-
-../src/lmrcImageBandPassFilter.c:
-
-../src/lmrcImageBilateralFilter.c:
-
-../src/lmrcImageBinarization.c:
-
-../src/lmrcImageBottomHatTransform.c:
-
-../src/lmrcImageBoundaryInfo.c:
-
-../src/lmrcImageCTFCompensation.c:
-
-../src/lmrcImageCTFDetermination.c:
-
-../src/lmrcImageCTFObservation.c:
-
-../src/lmrcImageCTFSN.c:
-
-../src/lmrcImageCVE.c:
-
-../src/lmrcImageCalcArea.c:
-
-../src/lmrcImageCenterGet.c:
-
-../src/lmrcImageCentre.c:
-
-../src/lmrcImageClosing.c:
-
-../src/lmrcImageClusterAnalysis.c:
-
-../src/lmrcImageCommonLine.c:
-
-../src/lmrcImageConnection.c:
-
-../src/lmrcImageConnectivityNumberCalc.c:
-
-../src/lmrcImageContourSurface.c:
-
-../src/lmrcImageContraction.c:
-
-../src/lmrcImageCorrelation.c:
- $lmrcImageEuclidDistanceCalc: Calculate Euclid distance between two images $
- $arg: in1: input mrcImage1 $
- $arg: in2: input mrcImage2 $
- $arg: mode: input int $
- $mode: 0 Sum of SQR $
- $mode: 1 Distance $
- $return: EuclidDistance $
-
-../src/lmrcImageCorrelationPVM.c:
-
-../src/lmrcImageCorrelationWithCTFCompensation.c:
-
-../src/lmrcImageCorrelationinSpace.c:
-
-../src/lmrcImageCrystalCreate.c:
-
-../src/lmrcImageDataMaxAndMinGetByImage.c:
-
-../src/lmrcImageDataStraightCopy.c:
-
-../src/lmrcImageDeconvolution.c:
-
-../src/lmrcImageDensity.c:
-
-../src/lmrcImageDensityInverse.c:
-
-../src/lmrcImageDensityNormalizationByImage.c:
-
-../src/lmrcImageDifferential.c:
-
-../src/lmrcImageDilation.c:
-
-../src/lmrcImageDistanceConversion.c:
-
-../src/lmrcImageEdge.c:
-
-../src/lmrcImageEdgeAverage.c:
-
-../src/lmrcImageEdgeEnhancement.c:
-
-../src/lmrcImageErosion.c:
-
-../src/lmrcImageFFT.c:
-
-../src/lmrcImageFOMCalc.c:
-
-../src/lmrcImageFeatureCalc.c:
-
-../src/lmrcImageFeatureExtraction.c:
-
-../src/lmrcImageFeatureExtractionCoOccurrence.c:
-
-../src/lmrcImageFeatureExtractionRunLength.c:
-
-../src/lmrcImageFilterCreate.c:
-
-../src/lmrcImageFirstNoiseReductionByRelaxation.c:
-
-../src/lmrcImageFloating.c:
-
-../src/lmrcImageFourierNeighborCorrelation.c:
-
-../src/lmrcImageFourierPowerSpectrum.c:
-
-../src/lmrcImageFourierShellCorrelation.c:
-
-../src/lmrcImageHighPassFilter.c:
-
-../src/lmrcImageHighlighting.c:
-
-../src/lmrcImageHoleFilling.c:
-
-../src/lmrcImageHoughTransform.c:
-
-../src/lmrcImageLabeling.c:
-
-../src/lmrcImageLocalMaximumValuesFind.c:
-
-../src/lmrcImageLogicalOperation.c:
-
-../src/lmrcImageLowPassFilter.c:
-
-../src/lmrcImageMasking.c:
-
-../src/lmrcImageMaxDataGet.c:
-
-../src/lmrcImageMirroring.c:
- $lmrcImageMirroring: (mrcImage* out, mrcImage* in, lmrcImageMirroring mode) $
-
-../src/lmrcImageModeChange.c:
-
-../src/lmrcImageModelCreate.c:
-
-../src/lmrcImageMontageCreate.c:
-
-../src/lmrcImageMorphology.c:
-
-../src/lmrcImageMove.c:
-
-../src/lmrcImageMultiCTFCompensation.c:
-
-../src/lmrcImageMultiplying.c:
-
-../src/lmrcImageNegativeLaplacian.c:
-
-../src/lmrcImageNoiseCreate.c:
-
-../src/lmrcImageNormalizing.c:
-
-../src/lmrcImageOneLineSimilarityCalc.c:
-
-../src/lmrcImageOpening.c:
-
-../src/lmrcImagePad.c:
-
-../src/lmrcImagePartImageSegmentation.c:
-
-../src/lmrcImagePattersonFunctionCalc.c:
-
-../src/lmrcImagePixelSummationOfProbabilityGetByImage.c:
-
-../src/lmrcImagePosterization.c:
-
-../src/lmrcImagePrewitt.c:
-
-../src/lmrcImageProjection.c:
-
-../src/lmrcImageProportionalDensityLevelSetByImage.c:
-
-../src/lmrcImageROI2D.c:
-
-../src/lmrcImageROI3D.c:
-
-../src/lmrcImageROInotChangeHeaderLength.c:
-
-../src/lmrcImageRadialDistribution.c:
-
-../src/lmrcImageRhoFiltering.c:
-
-../src/lmrcImageRoberts.c:
-
-../src/lmrcImageRotation.c:
-
-../src/lmrcImageSSDA.c:
-
-../src/lmrcImageSamplingUnitChange.c:
-
-../src/lmrcImageSecondNoiseReductionByRelaxation.c:
-
-../src/lmrcImageSecondNoiseReductionByRelaxationDijDimensionSet.c:
-
-../src/lmrcImageSecondNoiseReductionByRelaxationDijValueCalculate.c:
-
-../src/lmrcImageSecondNoiseReductionByRelaxationDijValueSet.c:
-
-../src/lmrcImageSecondNoiseReductionByRelaxationQValueSet.c:
-
-../src/lmrcImageSecondNoiseReductionByRelaxationRValueSet.c:
-
-../src/lmrcImageShapePCA.c:
-
-../src/lmrcImageShift.c:
-
-../src/lmrcImageShrink.c:
-
-../src/lmrcImageSigmaCalculate.c:
-
-../src/lmrcImageSinogram.c:
-
-../src/lmrcImageSinogramCorrelation.c:
-
-../src/lmrcImageSinogramFFT.c:
-
-../src/lmrcImageSmoothing.c:
-
-../src/lmrcImageSobel.c:
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-../src/lmrcImageSoftEdge.c:
-
-../src/lmrcImageSolventFlattening.c:
-
-../src/lmrcImageSpatialFrequencyFilter.c:
-
-../src/lmrcImageSphere.c:
-
-../src/lmrcImageSplit.c:
-
-../src/lmrcImageStack.c:
-
-../src/lmrcImageStudentCalculate.c:
-
-../src/lmrcImageSubtractionCalc.c:
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-../src/lmrcImageSummationCalculate.c:
-
-../src/lmrcImageSurfaceAreaCalc.c:
-
-../src/lmrcImageSymmetryFind.c:
-
-../src/lmrcImageTfunction.c:
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-../src/lmrcImageToneReversal.c:
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-../src/lmrcImageTopHatTransform.c:
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-../src/lmrcImageTrans.c:
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-../src/lmrcImageTransformDescartesIntoPolar.c:
-
-../src/lmrcImageTranspose.c:
-
-../src/lmrcImageTriming.c:
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-../src/lmrcImageUnsharpening.c:
-
-../src/lmrcImageVolumeCalc.c:
-
-../src/lmrcImageWindowing.c:
-
-../src/lmrcImagesFTest.c:
-
-../src/lmrcImagesStatDataGet.c:
-
-../src/lmrcImagesTTest.c:
-
-../src/lmrcImagesVarianceAnalysis.c:
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-../src/lmrcImagesVarianceMap.c:
-
-../src/lmrcMultiFFTCentralSectionsCompare.c:
-
-../src/lmrcMultiFFTCentralSectionsSigma.c:
-
-../src/lmrcSinogramFET.c:
-
-../src/lmrcSinogramFETPCA.c:
-
-../src/lmrcSinogramFETcalcWeight.c:
-
-../src/lmrcSinogramFETcorrelationMap.c:
-
-../src/lmrcSinogramFETnormalizedMap.c:
-
-../src/lmrcSinogramFETreferredCorrelation.c:
-
-../src/lmrcSinogramFETsmoothParameterMatching.c:
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-../src/mrcImageCheckFFT.c:
-
-../src/mrcImageCheckSameSize.c:
-
-../src/mrcImageCopy.c:
-
-../src/mrcImageDataSet.c:
-
-../src/mrcImageError.c:
-
-../src/mrcImageGet.c:
-
-../src/mrcImageGetPixels.c:
-
-../src/mrcImageInfo.c:
-
-../src/mrcImageInit.c:
-
-../src/mrcImageOperation.c:
-
-../src/mrcImagePVM.c:
-
-../src/mrcImagePrint.c:
-
-../src/mrcImageRead.c:
-
-../src/mrcImageSectionGet.c:
-
-../src/mrcImageSectionSet.c:
-
-../src/mrcImageSet.c:
-
-../src/mrcImageTailer.c:
-
-../src/mrcImageToIntImage.c:
-
-../src/mrcImageUtil.c:
-
-../src/mrcImageUtilityforVariance.c:
-
-../src/mrcImageWrite.c:
-
-../src/mrcImageWrite2.c:
-
-../src/mrcImagefuncmin.c:
-
-../src/mrcRefUtil.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/lmrcImageMeanFreePath.c:
-
-../src/lmrcImageShapeModePrint.c:
-
-../src/lmrcImageShapeSearch.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/lpdb2mrc2d.c:
-
-../src/lpdb2mrc3d.c:
-
-../src/lpdbCoord.c:
-
-../src/lpdbCoordInfo.c:
-
-../src/lpdbSelectedAtom.c:
-
-../src/lpdbSurface.c:
-
-../src/pdbFileRead.c:
-
-../src/pdbFileWrite.c:
-
-../src/pdbGet.c:
-
-../src/pdbInfoGet.c:
-
-../src/pdbRotation.c:
-
-../src/pdbSecondaryStructure.c:
-
-../src/pdbSet.c:
-
-../src/pdbTrans.c:
-
-../src/pdbUtil.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/tgaFileInit.c:
-
-../src/tgaFilePrint.c:
-
-../src/tgaFileRead.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/lAllCommonLineCalculation.c:
-
-../src/lAngularWeightCalculation.c:
-
-../src/lCommonLineCalculation.c:
-
-../src/lCommonLineDataSetInPlaneRotation.c:
-
-../src/lCommonLinesDataSet.c:
-
-../src/lDescartesIntoPolar.c:
-
-../src/lEvaluateCorrelationMapwithCommonLine.c:
-
-../src/lFETOrientationSearchByAnnealing.c:
-
-../src/lFETOrientationSearchByFeatureAlignment.c:
-
-../src/lFETOrientationSearchByFeatureAlignmentInitSet.c:
-
-../src/lFETOrientationSearchByFeatureAlignmentSphere.c:
-
-../src/lFETmapOrientationSearchBySimultaneousFitting.c:
-
-../src/lFETsmallMapSetCreate_forSimultaneousMinimization.c:
-
-../src/lInitialDataFileRead.c:
-
-../src/lJcalulation.c:
-
-../src/lLcalculation.c:
-
-../src/lPlaneRotationAngleSet.c:
-
-../src/lllDataSeparationInfoPrint.c:
-
-../src/lllDataSeparationInfoRead.c:
-
-../src/lllDataSeparationInfoSet.c:
-
-../src/lllDatarMaxLimitForSeparation.c:
-
-../src/lllExtract.c:
-
-../src/lllExtractCtfinfFileCreate.c:
-
-../src/lllExtractWithSeparation.c:
-
-../src/lllExtractdYEstimate.c:
-
-../src/lmrc2Dto3D.c:
-
-../src/lmrc2Dto3DSIRT.c:
-
-../src/lmrc3Dto2D.c:
-
-../src/lmrc3Dto2DFFT.c:
-
-../src/lmrcImageFileListAndEulerAngleDataRead.c:
-
-../src/lmrcImageOneLineGet.c:
-
-../src/lmrcImageSinogramCorrelationAdditionalWeight.c:
-
-../src/lmrcImageToFFT.c:
</PRE>
<HR>
<A NAME="include">
eosPThread \
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eosPoint \
eosString \
+eosXMAIL \
genUtil \
#LastSource
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/clusterLogAnalysis.c:
-
-../src/clusterLogInit.c:
-
-../src/clusterLogRead.c:
-
-../src/clusterLogUtil.c:
-
-../src/clusterLogWrite.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/crystalHelix.c:
- $Revision: 1.1 $
- $Date: 2002/02/14 10:18:46 $
- $Author: tacyas $
- $State: Exp $
- $Log: crystalHelix.c,v $
-
-../src/crystalInfoFile.c:
-
-../src/crystalInit.c:
-
-../src/crystalUtil.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/map2DCoordGet.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/matrix3DEulerAngleGet.c:
-
-../src/matrix3DEulerAngleSet.c:
-
-../src/matrix3DEulerAngles.c:
-
-../src/matrix3DFile.c:
-
-../src/matrix3DInit.c:
-
-../src/matrix3DMultiply.c:
-
-../src/matrix3DMultiplyMatrix.c:
-
-../src/matrix3DMultiplyVector.c:
-
-../src/matrix3DRotation.c:
-
-../src/matrix3DTranslation.c:
-
-../src/matrix3DUtil.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/memoryAllocate.c:
-
-../src/memoryByteSwap.c:
-
-../src/memoryClear.c:
-
-../src/memoryCopy.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/pvmStart.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/randomNormal.c:
-
-../src/randomUniform.c:
-
-../src/srandom.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/socketClient.c:
-
-../src/socketServer.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/pow2nn.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/Vector.c:
-
-../src/VectorRead.c:
-
-../src/VectorScalarProduct.c:
-
-../src/lVectorSpline2D.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/eosBayesCondition.c:
-
-../src/eosBayesDistributionInit.c:
-
-../src/eosBayesDistributionInitialProbabilitySet.c:
-
-../src/eosBayesEstimation.c:
-
-../src/eosBayesFree.c:
-
-../src/eosBayesParameterOfMaxPosterior.c:
-
-../src/eosBayesRead.c:
-
-../src/eosBayesWrite.c:
-
-../src/eosBayesflag.c:
-
-../src/leosBayesInit.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/eosFunc.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/eosPThread.c:
-
-../src/eosPThreadCreate.c:
-
-../src/eosPThreadInit.c:
-
-../src/eosPThreadJoin.c:
-
-../src/eosPThreadMutex.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/eosPointCopy.c:
-
-../src/eosPointProject.c:
-
-../src/eosPointRead.c:
-
-../src/eosPointRotate.c:
-
-../src/eosPointUtil.c:
-
-../src/eosPointWrite.c:
</PRE>
<HR>
<A NAME="include">
--- /dev/null
+SOURCE=\
+doc \
+inc \
+src \
+#LastSource
--- /dev/null
+SOURCE=\
+doc \
+inc \
+src \
+#LastSource
--- /dev/null
+OBJECTNAME = eosXMAIL
+EXTRA_INC =
+EXTRA_CCOPTS =
--- /dev/null
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+include Config/Define.inc
+
+DIRS = src inc doc
+
+all:
+ for dir in ${DIRS} ; \
+ do \
+ $(CD) $${dir}; $(MAKE) all; $(CD) ..; \
+ done
+
+install:
+ for dir in ${DIRS}; \
+ do \
+ ${CD} $${dir} ; $(MAKE) install; $(CD) ..; \
+ done
+
+debug:
+ for dir in ${DIRS} ; \
+ do \
+ $(CD) $${dir}; $(MAKE) debug; $(CD) ..; \
+ done
+
+install-debug:
+ for dir in ${DIRS}; \
+ do \
+ ${CD} $${dir} ; $(MAKE) install-debug; $(CD) ..; \
+ done
+
+clean:
+ for dir in ${DIRS} ; \
+ do \
+ $(CD) $${dir}; $(MAKE) clean; $(CD) ..; \
+ done
+
+depend:
+ for dir in ${DIRS} ; \
+ do \
+ $(CD) $${dir}; $(MAKE) depend; $(CD) ..; \
+ done
+
+put:
+ for dir in ${DIRS} ; \
+ do \
+ $(CD) $${dir}; $(MAKE) put; $(CD) ..; \
+ done
+
+check:
+ @cd src; \
+ if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+ echo making directory; \
+ mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+ fi
+ ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE);
+ @$(RM) -f src/Makefile
+ @$(RM) -f inc/Makefile
+ @$(RM) -f doc/Makefile
+ @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+ @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/inc/Makefile inc/Makefile
+ @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/doc/Makefile doc/Makefile
+ @rm -f src/.Depend src/.Source
+ @touch src/$(OSTYPE)/.Depend
+ @touch src/$(OSTYPE)/.Source
+ @touch src/.CCHeader
+ @touch src/.CHeader
+ @touch src/.Wish
+ @touch src/.Ruby
+ @cd inc; make install
+ @cd src; make install-ascii
+
+#
+# CVS
+#
+cvsupdate::
+ cvs -d $(EOS_CVSROOT) update -d
+
+cvscommit::
+ cvs -d $(EOS_CVSROOT) commit -R
+
+#
+# Backup
+#
+backup:
+ @cd ../../../.. ; \
+ echo $(OBJECTNAME) ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]*; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.*; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*
+
+backup-all:
+ @cd ../../../.. ; \
+ echo $(OBJECTNAME) ; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]*; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.*; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*
+
+#
+# Distribution
+#
+distribute:
+ @cd ../../../.. ; \
+ echo $(OBJECTNAME) ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]*; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.*; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]* ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+
+distribute-all:
+ @cd ../../../.. ; \
+ echo $(OBJECTNAME) ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]*; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.*; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]* ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+
+include Config/Target.inc
+
--- /dev/null
+include ../../../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+
+SOURCEDOC = $(OBJECTNAME).html
+DOCDSTDIR = $(EOS_HOME)/doc/Objects
+TARGETDOC = $(DOCDSTDIR)/$(SOURCEDOC)
+
+all: $(SOURCEDOC)
+
+install : $(TARGETDOC)
+
+$(TARGETDOC):$(SOURCEDOC)
+ $(INSTALL) -m 444 *.html $(DOCDSTDIR)
+ @cd $(DOCDSTDIR); make
+
+$(SOURCEDOC) : .$(SOURCEDOC) .header .footer ../inc/$(OBJECTNAME).h Makefile ../src/*.c
+ @echo Creating $(OBJECTNAME).html
+ @cat .header > $(SOURCEDOC)
+ @#htmlUpdateTime >> $(SOURCEDOC)
+ @cat .$(SOURCEDOC) >> $(SOURCEDOC)
+ @echo \<HR\> >> $(SOURCEDOC)
+ @echo "<A NAME=\"Information\">" >> $(SOURCEDOC)
+ @echo "<H2>Information from source codes</H2>" >> $(SOURCEDOC)
+ @echo "</A>" >> $(SOURCEDOC)
+ @echo "<PRE>" >> $(SOURCEDOC)
+ -@ident ../src/*.c >> $(SOURCEDOC)
+ @echo "</PRE>" >> $(SOURCEDOC)
+ @echo \<HR\> >> $(SOURCEDOC)
+ @echo \<A NAME=\"include\"\>>> $(SOURCEDOC)
+ @echo "<H2>$(OBJECTNAME).h</H2>">> $(SOURCEDOC)
+ @echo \</A\> >>$(SOURCEDOC)
+ @echo \<PRE\> >> $(SOURCEDOC)
+ @cat ../inc/$(OBJECTNAME).h >> $(SOURCEDOC)
+ @echo \</PRE\> >> $(SOURCEDOC)
+ @cat .footer >> $(SOURCEDOC)
+
+clean:
+
+depend:
--- /dev/null
+include ../../../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+
+INCFILE = $(OBJECTNAME).h
+
+all:
+
+install:$(EOS_HOME)/include/$(INCFILE)
+
+$(EOS_HOME)/include/$(INCFILE):$(INCFILE)
+ if [ ! -d $(EOS_HOME)/include ] ; then \
+ mkdir $(EOS_HOME)/include ; \
+ fi
+ $(INSTALL) -m 444 $(INCFILE) $(EOS_HOME)/include/
+
+clean:
+ $(RM) -f *.bak
+
+depend:
+ $(RM) -f *.bak
+
+cvsupdate::
+ cvs -d $(EOS_CVSROOT) update
+
+cvscommit::
+ @echo "cvs -d $(EOS_CVSROOT) commit"
+
+cvsadd::
+ @echo "cvs -d $(EOS_CVSROOT) add"
--- /dev/null
+CCHeader = \
+
--- /dev/null
+CHeader = \
+
--- /dev/null
+Ruby = \
+
--- /dev/null
+Wish = \
+
--- /dev/null
+SHELL=/bin/ksh
+include ../Config/Define.inc
+include ../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../../../Config/Define.inc
+
+include $(OSTYPE)/.Source
+include .CHeader
+include .CCHeader
+include .Wish
+include .Ruby
+
+LIBNAME=lib$(OBJECTNAME).a
+SHAREDLIB=lib$(OBJECTNAME).so
+LIBNAMEDEBUG=lib$(OBJECTNAME).debug.a
+
+DSTDIR=../../../../../lib/$(OSTYPE)/
+SOURCE=$(OSTYPE)/.Source
+ARCHTEMPLATEDIR=$(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH
+
+all: hostdepend static-lib shared-lib ruby-lib debug
+ @echo LIBNAME:$(LIBNAME)
+ @echo OBJECTNAME:$(OBJECTNAME)
+
+hostdepend:
+ @if [ ! -L $(OSTYPE) ] ; then \
+ moveHostdependent ; \
+ fi
+
+debug: debug-lib
+
+static-lib::
+ @echo static-lib:LIBNAME:$(LIBNAME) ; \
+ $(RM) -f $(OSTYPE)/Makefile; \
+ $(CP) $(ARCHTEMPLATEDIR)/Makefile $(OSTYPE)/Makefile ; \
+ cd $(OSTYPE); \
+ $(MAKE) $(LIBNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME) WORLDNAME=$(WORLDNAME)
+
+shared-lib::
+ @echo shared-lib:LIBNAME:$(LIBNAME) ; \
+ $(RM) -f $(OSTYPE)/Makefile; \
+ $(CP) $(ARCHTEMPLATEDIR)/Makefile $(OSTYPE)/Makefile ; \
+ cd $(OSTYPE); \
+ $(MAKE) $(SHAREDLIB) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME) WORLDNAME=$(WORLDNAME)
+
+ruby-lib::
+ @if [ -d Swig ]; then \
+ echo "--- Swig ---"; \
+ cd Swig; \
+ if [ -f extconf.rb ] ; then \
+ swig -ruby -I/usr/include -I$(EOS_HOME)/include *.i ; \
+ ruby extconf.rb --with-Eos-include=$(EOS_HOME)/include --with-Eos-lib=$(EOS_HOME)/lib/$(OSTYPE) --with-opt-lib=$LD_LIBRARY_PATH --with-opt-lib=$(EOS_HOME)/util/$(OSTYPE)/lib --with-GL-lib=/usr/lib ; \
+ make ; \
+ make sitearchdir=$(EOS_HOME)/lib/$(OSTYPE) install; \
+ fi ; \
+ fi
+
+debug-lib::
+ @cd $(OSTYPE); \
+ $(RM) -f Makefile; \
+ $(CP) $(ARCHTEMPLATEDIR)/Makefile Makefile ; \
+ $(MAKE) $(LIBNAMEDEBUG) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME) WORLDNAME=$(WORLDNAME)
+
+clean:
+ rm -f *.[oa] *.debugo *.cudagdbo *.so *.sharedo *.linkinfo $(OSTYPE)/*.[ao] $(OSTYPE)/*.debugo $(OSTYPE)/*.cudagdbo $(OSTYPE)/*.linkinfo *.bak core $(OSTYPE)/*.sharedo $(OSTYPE)/*.so
+
+Makefile:
+ touch .Source
+ touch .CHeader
+ touch .CCHeader
+
+install: all install-static install-shared install-ascii
+ @echo "Installation has completed: $(LIBNAME)"
+
+install-static: $(DSTDIR)/$(LIBNAME)
+install-shared: $(DSTDIR)/$(SHAREDLIB)
+
+install-debug: debug $(DSTDIR)/$(LIBNAMEDEBUG) install-ascii
+ @echo "Installation has completed: $(LIBNAMEDEBUG)"
+
+install-ascii: h hh wish ruby
+
+h:
+ @if [ -n "$(CHeader)" ] ; \
+ then\
+ echo "C Header Install" ; \
+ for file in $(CHeader) dummy ; \
+ do \
+ if [ -f $${file} ] ; \
+ then\
+ echo $${file}; $(INSTALL) -m 444 $${file} $(EOS_HOME)/include ; \
+ fi;\
+ done; \
+ fi
+
+hh:
+ @if [ -n "$(CCHeader)" ] ; \
+ then \
+ echo "C++ Header Install" ; \
+ for file in $(CCHeader) dummy ; \
+ do \
+ if [ -f $${file} ] ; \
+ then\
+ echo $${file}; $(INSTALL) -m 444 $${file} $(EOS_HOME)/include ; \
+ fi;\
+ done; \
+ fi
+
+wish:
+ @if [ -n "$(Wish)" ] ; \
+ then \
+ echo "Wish Install" ; \
+ for file in $(Wish) dummy ; \
+ do \
+ if [ -f $${file} ] ; \
+ then\
+ echo $${file}; $(INSTALL) -m 444 $${file} $(EOS_HOME)/lib ; \
+ fi;\
+ done; \
+ fi
+
+ruby:
+ @if [ -n "$(Ruby)" ] ; \
+ then \
+ echo "Ruby Install" ; \
+ for file in $(Ruby) dummy ; \
+ do \
+ if [ -f $${file} ] ; \
+ then\
+ echo $${file}; $(INSTALL) -m 444 $${file} $(EOS_HOME)/lib ; \
+ fi;\
+ done; \
+ fi
+
+put:
+ @Files=`ls -l | grep $${USER} | grep rw | grep -e "\.c" ` ;\
+ for file in $${Files} dummy; \
+ do \
+ if [ -w $${file} ] ; \
+ then\
+ echo $${file}; sccsPut $${file} ; \
+ fi;\
+ done
+
+$(DSTDIR)/$(LIBNAME): static-lib
+ @echo Installing lib: $(LIBNAME)
+ @if [ ! -d $(DSTDIR) ] ; then mkdir $(DSTDIR) ; fi
+ @cd $(OSTYPE); $(INSTALL) -m 444 $(LIBNAME) ../$(DSTDIR)
+ @echo LIBNAME:$(LIBNAME)
+ @echo Link EosObjects
+ @OBJLIST=`ls $(OSTYPE)/*.o `;\
+ echo $${OBJLIST} | sed -f ../../../../Config/o2nl.sed > .tmp1 ; \
+ echo $(REALOBJ) | sed -f ../../../../Config/o2nl.sed > .tmp2 ; \
+ echo "#### Attention Uncompiled file ####";\
+ comm -13 .tmp1 .tmp2 ; \
+ echo "########";\
+ echo $(AR) r $(DSTDIR)/libEosObjects.a $${OBJLIST} ; \
+ $(AR) r $(DSTDIR)/libEosObjects.a $${OBJLIST}; \
+ echo $(AR) s $(DSTDIR)/libEosObjects.a ; \
+ $(AR) s $(DSTDIR)/libEosObjects.a \
+ chmod 660 $(DSTDIR)/libEosObjects.a
+ @rm .tmp1 .tmp2
+
+$(DSTDIR)/$(LIBNAMEDEBUG): debug
+ @echo Installing lib: $(LIBNAMEDEBUG)
+ @if [ ! -d $(DSTDIR) ] ; then mkdir $(DSTDIR) ; fi
+ @cd $(OSTYPE); $(INSTALL) -m 444 $(LIBNAMEDEBUG) ../$(DSTDIR)
+ @echo LIBNAME:$(LIBNAMEDEBUG)
+ @echo Link EosObjects
+ @OBJLISTDEBUG=`ls $(OSTYPE)/*.debugo `;\
+ echo $${OBJLISTDEBUG} | sed -f ../../../../Config/o2nl.sed > .tmp1 ; \
+ echo $(REALOBJDEBUG) | sed -f ../../../../Config/o2nl.sed > .tmp2 ; \
+ echo "#### Attention Uncompiled file ####";\
+ comm -13 .tmp1 .tmp2 ; \
+ echo "########";\
+ echo $(AR) r $(DSTDIR)/libEosObjects.debug.a $${OBJLISTDEBUG} ; \
+ $(AR) r $(DSTDIR)/libEosObjects.debug.a $${OBJLISTDEBUG};
+ echo $(AR) s $(DSTDIR)/libEosObjects.debug.a ; \
+ $(AR) s $(DSTDIR)/libEosObjects.debug.a
+ chmod 660 $(DSTDIR)/libEosObjects.debug.a
+ @rm .tmp1 .tmp2
+
+$(DSTDIR)/$(SHAREDLIB): shared-lib
+ @echo Installing lib: $(SHAREDLIB)
+ @if [ ! -d $(DSTDIR) ] ; then mkdir $(DSTDIR) ; fi
+ @cd $(OSTYPE); $(INSTALL) -m 444 $(SHAREDLIB) ../$(DSTDIR)
+ @echo LIBNAME:$(SHAREDLIB)
+ @echo Link EosObjects
+ @OBJLIST=`ls $(OSTYPE)/*.sharedo `;\
+ echo $${OBJLIST} | sed -f ../../../../Config/o2nl.sed > .tmp1 ; \
+ echo $(REALSHAREDOBJ) | sed -f ../../../../Config/o2nl.sed > .tmp2 ; \
+ echo "#### Attention Uncompiled file ####";\
+ comm -13 .tmp1 .tmp2 ; \
+ echo "########"; \
+ if [ ! -d $(DSTDIR)/shared ] ; then \
+ mkdir $(DSTDIR)/shared; \
+ fi; \
+ $(CP) $${OBJLIST} $(DSTDIR)/shared ; \
+ echo "$(CP) $${OBJLIST} $(DSTDIR)/shared" ; \
+ $(SHARED) $(DSTDIR)/libEosObjects.so $(DSTDIR)/shared/*.sharedo ; \
+ echo "$(SHARED) $(DSTDIR)/libEosObjects.so $(DSTDIR)/shared/*.sharedo" ; \
+ chmod 660 $(DSTDIR)/libEosObjects.so
+ @rm .tmp1 .tmp2
+
+install-all:
+ @cd .. ; $(MAKE) install
+
+install-ruby: ruby-lib
+ cd $(OSTYPE); $(RUBY) -r ftools -e 'File::install(ARGV[0], ARGV[1], 0555, true)' $(SHAREDLIB) $(RUBYSHAREDLIB)/$(SHAREDLIB)
+
+depend:
+ @echo dependency checking now
+ @echo $(OSTYPE)
+ @echo SRC = \\ > $(SOURCE)
+ @ls -1 *.c | sed -e "s/\.c/.c \\\\/" >> $(SOURCE)
+ @ls -1 *.cc | sed -e "s/\.cc/.cc \\\\/" >> $(SOURCE)
+ @ls -1 *.ccm | sed -e "s/\.ccm/.ccm \\\\/" >> $(SOURCE)
+ @ls -1 *.idl | sed -e "s/\.idl/.idl \\\\/" >> $(SOURCE)
+ @ls -1 *.cu | sed -e "s/\.cu/.cu \\\\/" >> $(SOURCE)
+ @echo >> $(SOURCE)
+ @#
+ @echo OBJ = \\ >> $(SOURCE)
+ @ls -1 *.c | sed -e "s/\.c/.o \\\\/" >> $(SOURCE)
+ @ls -1 *.cc | sed -e "s/\.cc/.o \\\\/" >> $(SOURCE)
+ @ls -1 *.ccm | sed -e "s/\.ccm/.o \\\\/" >> $(SOURCE)
+ @ls -1 *.idl | sed -e "s/\.idl/.o \\\\/" >> $(SOURCE)
+ @ls -1 *.cu | sed -e "s/\.cu/.o \\\\/" >> $(SOURCE)
+ @echo >> $(SOURCE)
+ @#
+ @echo SHAREDOBJ = \\ >> $(SOURCE)
+ @ls -1 *.c | sed -e "s/\.c/.sharedo \\\\/" >> $(SOURCE)
+ @ls -1 *.cc | sed -e "s/\.cc/.sharedo \\\\/" >> $(SOURCE)
+ @ls -1 *.ccm | sed -e "s/\.ccm/.sharedo \\\\/" >> $(SOURCE)
+ @ls -1 *.idl | sed -e "s/\.idl/.sharedo \\\\/" >> $(SOURCE)
+ @ls -1 *.cu | sed -e "s/\.cu/.sharedo \\\\/" >> $(SOURCE)
+ @echo >> $(SOURCE)
+ @#
+ @echo REALOBJ = \\ >> $(SOURCE)
+ @ls -1 *.c | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.c/.o \\\\/" >> $(SOURCE)
+ @ls -1 *.cc | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.cc/.o \\\\/" >> $(SOURCE)
+ @ls -1 *.ccm | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.ccm/.o \\\\/" >> $(SOURCE)
+ @ls -1 *.idl | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.idl/.o \\\\/" >> $(SOURCE)
+ @ls -1 *.cu | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.cu/.o \\\\/" >> $(SOURCE)
+ @echo >> $(SOURCE)
+ @echo REALSHAREDOBJ = \\ >> $(SOURCE)
+ @ls -1 *.c | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.c/.sharedo \\\\/" >> $(SOURCE)
+ @ls -1 *.cc | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.cc/.sharedo \\\\/" >> $(SOURCE)
+ @ls -1 *.ccm | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.ccm/.sharedo \\\\/" >> $(SOURCE)
+ @ls -1 *.idl | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.idl/.sharedo \\\\/" >> $(SOURCE)
+ @ls -1 *.cu | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.cu/.sharedo \\\\/" >> $(SOURCE)
+ @echo >> $(SOURCE)
+ @echo OBJDEBUG = \\ >> $(SOURCE)
+ @ls -1 *.c | sed -e "s/\.c/.debugo \\\\/" >> $(SOURCE)
+ @ls -1 *.cc | sed -e "s/\.cc/.debugo \\\\/" >> $(SOURCE)
+ @ls -1 *.ccm | sed -e "s/\.ccm/.debugo \\\\/" >> $(SOURCE)
+ @ls -1 *.idl | sed -e "s/\.idl/.debugo \\\\/" >> $(SOURCE)
+ @echo >> $(SOURCE)
+ @#
+ @echo REALOBJDEBUG = \\ >> $(SOURCE)
+ @ls -1 *.c | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.c/.debugo \\\\/" >> $(SOURCE)
+ @ls -1 *.cc | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.cc/.debugo \\\\/" >> $(SOURCE)
+ @ls -1 *.ccm | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.ccm/.debugo \\\\/" >> $(SOURCE)
+ @ls -1 *.idl | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.idl/.debugo \\\\/" >> $(SOURCE)
+ @ls -1 *.cu | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.cu/.debugo \\\\/" >> $(SOURCE)
+ @echo >> $(SOURCE)
+ @echo OBJCUDAGDB = \\ >> $(SOURCE)
+ @ls -1 *.c | sed -e "s/\.c/.cudagdb.o \\\\/" >> $(SOURCE)
+ @ls -1 *.cc | sed -e "s/\.cc/.cudagdb.o \\\\/" >> $(SOURCE)
+ @ls -1 *.cu | sed -e "s/\.cu/.cudagdb.o \\\\/" >> $(SOURCE)
+ @echo >> $(SOURCE)
+ @#
+ @echo REALOBJCUDAGDB = \\ >> $(SOURCE)
+ @ls -1 *.c | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.c/.cudagdb.o \\\\/" >> $(SOURCE)
+ @ls -1 *.cc | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.cc/.cudagdb.o \\\\/" >> $(SOURCE)
+ @ls -1 *.cu | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.cu/.cudagdb.o \\\\/" >> $(SOURCE)
+ @echo >> $(SOURCE)
+ @#
+ @echo >> $(SOURCE)
+ @echo CCHeader = \\ > .CCHeader
+ @ls -1 *.hh | sed -e "s/\.hh/.hh \\\\/" >> .CCHeader
+ @echo >> .CCHeader
+ @#
+ @echo CHeader = \\ > .CHeader
+ @ls -1 *.h | sed -e "s/\.h/.h \\\\/" >> .CHeader
+ @echo >> .CHeader
+ @#
+ @echo Wish = \\ > .Wish
+ @ls -1 *.wish | sed -e "s/\.wish/.wish \\\\/" >> .Wish
+ @echo >> .Wish
+ @#
+ @echo Ruby = \\ > .Ruby
+ @ls -1 *.rb | sed -e "s/\.rb/.rb \\\\/" >> .Ruby
+ @echo >> .Ruby
+ @#
+ @ls -1 *.c *.cc *.ccm | \
+ awk -vHostType=$(OSTYPE) -f$(EOS_HOME)/sbin/awk/objectdependency.awk > $(OSTYPE)/.Depend
+ @#
+ @$(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(KHOROS_INCS) *.c *.cc *.ccm >> $(OSTYPE)/.Depend
+ @for file in $(SRC) dummy ; \
+ do \
+ if [ -f $${file} ] ; \
+ then \
+ echo $${file} ; \
+ ln -sf ../$${file} $(OSTYPE)/$${file}; \
+ fi ;\
+ done
+
+#
+#
+#
+test::
+ @if [ -d test ] ; then \
+ cd test; \
+ $(MAKE); \
+ else \
+ echo "No test directory: making test"; \
+ mkdir test; \
+ cd test; \
+ touch Makefile; \
+ fi
+
+#
+# cvs
+#
+cvsupdate::
+ cvs -d $(EOS_CVSROOT) update -d
+
+cvslogin::
+ cvs -d $(EOS_CVSROOT) login
+
+cvscommit::
+ @echo "cvs -d $(EOS_CVSROOT) commit -m @"message@" filename"
+
+cvsadd::
+ @echo "cvs -d $(EOS_CVSROOT) add filename|dirname"
+ @echo "Need Commit for filename"
+ @echo "make cvscommit"
+
+cvsremove::
+ @echo "cvs -d $(EOS_CVSROOT) remove filename"
+ @echo "Need Commit for filename"
+ @echo "make cvscommit"
+
+include $(OSTYPE)/.Depend
+include ../Config/Target.inc
--- /dev/null
+../../../../../hostdepend/X86MAC64/src/Objects/General/eosXMAIL/src/X86MAC64
\ No newline at end of file
-/bin/bash: dcdCompareCA: そのようなファイルやディレクトリはありません
+/bin/bash: dcdCompareCA: No such file or directory
-/bin/bash: dcdDistanceAtomBetweenAtom: そのようなファイルやディレクトリはありません
+/bin/bash: dcdDistanceAtomBetweenAtom: No such file or directory
-/bin/bash: Display2: そのようなファイルやディレクトリはありません
+dyld: Library not loaded: @rpath/libtk8.6.dylib
+ Referenced from: /Applications/Eos/src/Tools/Integration/Display2/src/Display2
+ Reason: image not found
-/bin/bash: Display3: そのようなファイルやディレクトリはありません
+/bin/bash: Display3: No such file or directory
-/bin/bash: Eos: そのようなファイルやディレクトリはありません
+/bin/bash: Eos: No such file or directory
-/bin/bash: StereoDisplay: そのようなファイルやディレクトリはありません
+/bin/bash: StereoDisplay: No such file or directory
-/bin/bash: Visualmake: そのようなファイルやディレクトリはありません
+/bin/bash: Visualmake: No such file or directory
-/bin/bash: ctfDisplay: そのようなファイルやディレクトリはありません
+dyld: Library not loaded: @rpath/libtk8.6.dylib
+ Referenced from: /Applications/Eos/src/Tools/Integration/ctfDisplay/src/ctfDisplay
+ Reason: image not found
-/bin/bash: imagesClustering: そのようなファイルやディレクトリはありません
+/bin/bash: imagesClustering: No such file or directory
-/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
+dyld: Library not loaded: @rpath/libtk8.6.dylib
+ Referenced from: /Applications/Eos/src/Tools/Integration/imagesView/src/imagesView
+ Reason: image not found
-/bin/bash: obj3Don2DImageView: そのようなファイルやディレクトリはありません
+/bin/bash: obj3Don2DImageView: No such file or directory
-/bin/bash: smolet: そのようなファイルやディレクトリはありません
+/bin/bash: smolet: No such file or directory
-/bin/bash: ctfDeterminationByBayes: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>ctfDeterminationByBayes</TITLE>
+</HEAD>
+<BODY>
+<H1>ctfDeterminationByBayes</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ctfDeterminationByBayes
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i[nput]2 In2 (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i[nput]3 In3 (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i[nput]4 In4 (NULL ).as(inFileListNoOpen ) ] :Essential :InputDataFile
+ [-n[um] numDistribution (3 ).as(Integer )
+ numLikelihood (3 ).as(Integer ) ] :Essential :Integer
+ [-rmax rmax (250 ).as(Real ) ] :Optional :rmax[1/A]
+ [-rintermediate rintermediate (250 ).as(Real ) ] :Optional :rintermediate[1/A]
+ [-rfiestpeak rfirstpeak (0.001 ).as(Real ) ] :Optional :rfirstpeak[1/A]
+ [-rmin rmin (0 ).as(Real ) ] :Optional :rmin[1/A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-MTFmode MTFmode (0 ).as(Integer ) ] :Optional :MTFmode
+ [-Ainmode Ainmode (0 ).as(Integer ) ] :Optional :Ainmode
+ [-Intensitymode Intensitymode (0 ).as(Integer ) ] :Optional :Intensitymode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: ctfDeterminationFromPhaseComparison: そのようなファイルやディレクトリはありません
+/bin/bash: ctfDeterminationFromPhaseComparison: No such file or directory
-/bin/bash: ctfDeterminationFromThonRing: そのようなファイルやディレクトリはありません
+/bin/bash: ctfDeterminationFromThonRing: No such file or directory
-/bin/bash: ctfFunctionServer: そのようなファイルやディレクトリはありません
+/bin/bash: ctfFunctionServer: No such file or directory
-/bin/bash: ctfMultiFunction: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>ctfMultiFunction</TITLE>
+</HEAD>
+<BODY>
+<H1>ctfMultiFunction</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ctfMultiFunction
+Options:
+ [-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
+ 1: PhaseCTF + ratio*AmpCTF
+ 32: EnvFromAillumination*()
+>>>> File Format <<<<
+Defocus[A] Cs[mm] AccV[kV] AmplitudeContrast
+Info file was made by llExtractWithLayerSeparationFilamentInfo -oI
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: ctfZeroPoint: そのようなファイルやディレクトリはありません
+/bin/bash: ctfZeroPoint: No such file or directory
-/bin/bash: defocusDeterminationFromThonRing: そのようなファイルやディレクトリはありません
+/bin/bash: defocusDeterminationFromThonRing: No such file or directory
-/bin/bash: tiltInfoDetermine: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>tiltInfoDetermine</TITLE>
+</HEAD>
+<BODY>
+<H1>tiltInfoDetermine</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: tiltInfoDetermine
+Options:
+ [-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>
+</HTML>
-/bin/bash: homology2PG: そのようなファイルやディレクトリはありません
+/bin/bash: homology2PG: No such file or directory
-/bin/bash: pgDataBaseSelectServer: そのようなファイルやディレクトリはありません
+/bin/bash: pgDataBaseSelectServer: No such file or directory
-/bin/bash: pgJournalSelect: そのようなファイルやディレクトリはありません
+/bin/bash: pgJournalSelect: No such file or directory
-/bin/bash: pgJournalSelectCORBAClient: そのようなファイルやディレクトリはありません
+/bin/bash: pgJournalSelectCORBAClient: No such file or directory
-/bin/bash: pgJournalSelectCORBAServer: そのようなファイルやディレクトリはありません
+/bin/bash: pgJournalSelectCORBAServer: No such file or directory
-/bin/bash: pgMemoSelectCORBAServer: そのようなファイルやディレクトリはありません
+/bin/bash: pgMemoSelectCORBAServer: No such file or directory
-/bin/bash: pgSelect: そのようなファイルやディレクトリはありません
+/bin/bash: pgSelect: No such file or directory
-/bin/bash: eosBayesInit: そのようなファイルやディレクトリはありません
+/bin/bash: eosBayesInit: No such file or directory
-/bin/bash: eosPointCurvatureInfo: そのようなファイルやディレクトリはありません
+/bin/bash: eosPointCurvatureInfo: No such file or directory
-/bin/bash: eosPointProjector: そのようなファイルやディレクトリはありません
+/bin/bash: eosPointProjector: No such file or directory
-/bin/bash: eosPointRotation: そのようなファイルやディレクトリはありません
+/bin/bash: eosPointRotation: No such file or directory
-/bin/bash: moi2mrc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>moi2mrc</TITLE>
+</HEAD>
+<BODY>
+<H1>moi2mrc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: moi2mrc
+Options:
+ [-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>
+</BODY>
+</HTML>
-/bin/bash: mrc2gif: そのようなファイルやディレクトリはありません
+dyld: Library not loaded: @rpath/libgif.dylib
+ Referenced from: /Applications/Eos/src/Tools/filter/mrc2gif/src/mrc2gif
+ Reason: image not found
-/bin/bash: mrc2lattice: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2lattice: No such file or directory
-/bin/bash: mrc2pov: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2pov: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>mrc2tiff</TITLE>
-</HEAD>
-<BODY>
-<H1>mrc2tiff</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrc2tiff
-Options:
- [-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 ---
-Previously, the black and white were inter-changed between mrc and tiff. Now they are not changed
-</PRE>
-</BODY>
-</HTML>
+dyld: Library not loaded: @rpath/libtiff.dylib
+ Referenced from: /Applications/Eos/src/Tools/filter/mrc2tiff/src/mrc2tiff
+ Reason: Incompatible library version: mrc2tiff requires version 12.0.0 or later, but libtiff.dylib provides version 8.0.0
-/bin/bash: mrc2viff: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2viff: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>tiff2mrc</TITLE>
-</HEAD>
-<BODY>
-<H1>tiff2mrc</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: tiff2mrc
-Options:
- [-i[nput] inFile (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-o[utput] outFile (NULL ).as(outFile ) ] :Essential :OutputDataFile
- [-r[esolution] Resolution (1.0 ).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
- R: 00
- G: 10
- B: 20
-</PRE>
-</BODY>
-</HTML>
+dyld: Library not loaded: @rpath/libtiff.dylib
+ Referenced from: /Applications/Eos/src/Tools/filter/tiff2mrc/src/tiff2mrc
+ Reason: Incompatible library version: tiff2mrc requires version 12.0.0 or later, but libtiff.dylib provides version 8.0.0
-/bin/bash: hf2000Init: そのようなファイルやディレクトリはありません
+/bin/bash: hf2000Init: No such file or directory
-/bin/bash: hf2000LenzCurrent: そのようなファイルやディレクトリはありません
+/bin/bash: hf2000LenzCurrent: No such file or directory
-/bin/bash: hf2000SpecimenPosition: そのようなファイルやディレクトリはありません
+/bin/bash: hf2000SpecimenPosition: No such file or directory
-/bin/bash: khorosFilterGenerate: そのようなファイルやディレクトリはありません
+/bin/bash: khorosFilterGenerate: No such file or directory
-/bin/bash: llDataAxisSearch: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>llDataAxisSearch</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataAxisSearch</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataAxisSearch
+Options:
+ [-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
+..........
+
+----- Control File -----
+In1[inFile:NULL] #In: NearSide
+In2[inFile:NULL] #In: FarSide
+Out1[outFile:NULL] #Out: NearSide
+Out2[outFile:NULL] #Out: FarSide
+Avg[outFile:NULL] #Out: Average
+Out[outFile:NULL] #Out: FitParam
+truePitch[Real:NULL] #TruePitch[A]
+L[inFile:NULL] #LayerInfo
+Omin[Real:0.0] Omax[Real:0.0] Odelta[Real:1.0] #Omega[degree]
+xmin[Real:-10.0] xmax[Real:10.0] xdelta[Real:0.1] #shiftx[A]
+R[Real:10.0] #Resolution[A]
+mode[Integer:0] #Mode
+----- Inside Axis Search Parameter File -----
+info.In1, info.In2, paraFit.Para.R*DEGREE, paraFit.Para.x.Value, paraFit.Para.Omega.Value
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: llDataCTFCompensate: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>llDataCTFCompensate</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataCTFCompensate</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataCTFCompensate
+Options:
+ [-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,
+.................................................
+RRn Fn PHIn : If RRn<= R , F*0 PHI = 0
+----- Control File -----
+In[inFile:NULL] #InputDataFile
+In1[inFile:NULL] #InputCTFInformation
+Out[outFile:NULL] #OutputDataFile
+truePitch[Real:100.0] #truePitch[A]
+mode[Integer:0] #Mode
+----- CTFInformation file 2 -----
+dF[A] Cs[mm] Acc[kV] ratioOfAmpToPhase
+----- How to make file 1 or file 2 -----
+llExtractCtfinfFileCreate make these files.
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: llDataFitServer: そのようなファイルやディレクトリはありません
+/bin/bash: llDataFitServer: No such file or directory
-/bin/bash: llDataMultiCTFCompensation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>llDataMultiCTFCompensation</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataMultiCTFCompensation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataMultiCTFCompensation
+Options:
+ [-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 -----
+ 0: |CTFi|/Sigma(SQR(CTFi))
+ 1: CTFi /Sigma(SQR(CTFi))
+</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
+dyld: Library not loaded: @rpath/libtk8.6.dylib
+ Referenced from: /Applications/Eos/src/Tools/llData/llDataPrint/src/llDataPrint
+ Reason: image not found
-/bin/bash: llDataRotation: そのようなファイルやディレクトリはありません
+/bin/bash: llDataRotation: No such file or directory
-/bin/bash: llDataSeparate: そのようなファイルやディレクトリはありません
+/bin/bash: llDataSeparate: No such file or directory
-/bin/bash: matrix3DEulerAngleTransform: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>matrix3DEulerAngleTransform</TITLE>
+</HEAD>
+<BODY>
+<H1>matrix3DEulerAngleTransform</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: matrix3DEulerAngleTransform
+Options:
+ [-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>
+</BODY>
+</HTML>
-/bin/bash: matrix3DFromEulerAngle: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>matrix3DFromEulerAngle</TITLE>
+</HEAD>
+<BODY>
+<H1>matrix3DFromEulerAngle</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: matrix3DFromEulerAngle
+Options:
+ [-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>
+</HTML>
-/bin/bash: matrix3DInverse: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>matrix3DInverse</TITLE>
+</HEAD>
+<BODY>
+<H1>matrix3DInverse</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: matrix3DInverse
+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: fft2d: そのようなファイルやディレクトリはありません
+/bin/bash: fft2d: No such file or directory
-/bin/bash: mrc2dsn6: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2dsn6: No such file or directory
-/bin/bash: mrc2hdf: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2hdf: No such file or directory
-/bin/bash: mrcFFTCTFCompensation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTCTFCompensation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTCTFCompensation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTCTFCompensation
+Options:
+ [-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 :
+...................................
+RRn Fn : If RRn<=R, Fn
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrcFFTCentralSection: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTCentralSection</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTCentralSection</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTCentralSection
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input: mrc(3D)
+ [-t[emplate] Template (NULL ).as(inFile::mrcImage ) ] :Optional :Input: mrcFFT(2D)
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output: mrcFFT(2D)
+ [-o[utput]I[mage] OutImage (NULL ).as(outFile::mrcImage ) ] :Optional :Output: mrcImage(2D)
+ [-E[uler]A[ngle] EAMode (YOYS ).as(String )
+ Rot1 (0.0 ).as(Real )
+ Rot2 (0.0 ).as(Real )
+ Rot3 (0.0 ).as(Real ) ] :Optional :EulerAngle
+ [-trans[late] TransX (0.0 ).as(Real )
+ TransY (0.0 ).as(Real ) ] :Optional :Traslation(2D)
+ [-InterpMode InterpMode (0 ).as(Integer ) ] :Optional :Interpolation Mode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+-t[emplate] : If not set, the size of out (Nx, Ny) is set as the size of in (Nx, Ny).</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrcFFTCentralSectionCompare: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTCentralSectionCompare</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTCentralSectionCompare</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTCentralSectionCompare
+Options:
+ [-i[nput] In2D (NULL ).as(inFile::mrcImage ) ] :Essential :Input: 2D(FFT)
+ [-i[nput]3d In3D (NULL ).as(inFile::mrcImage ) ] :Essential :Input: 3D(FFT)
+ [-E[uler]A[ngle] EAMode (YOYS ).as(String )
+ Rot1 (0.0 ).as(Real )
+ Rot2 (0.0 ).as(Real )
+ Rot3 (0.0 ).as(Real ) ] :Optional :Input: EulerAngle
+ [-trans[late] TransX (0.0 ).as(Real )
+ TransY (0.0 ).as(Real ) ] :Optional :Input: Translation
+ [-InterpMode InterpMode (0 ).as(Integer ) ] :Optional :Interpolation Mode
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output:Likelihood
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrcFFTIQEstimation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTIQEstimation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTIQEstimation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTIQEstimation
+Options:
+ [-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>
+</HTML>
-/bin/bash: mrcImage1dCutAverage: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImage1dCutAverage: No such file or directory
-/bin/bash: mrcImage3DCTFObservation: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImage3DCTFObservation: No such file or directory
-/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
+/bin/bash: mrcImage3DPeakGet: No such file or directory
-/bin/bash: mrcImageAutoFilamentExtract: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageAutoFilamentExtract: No such file or directory
-/bin/bash: mrcImageAutoRotationCorrelationResultPrint: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageAutoRotationCorrelationResultPrint: No such file or directory
-/bin/bash: mrcImageAutoTriming: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageAutoTriming: No such file or directory
-/bin/bash: mrcImageCTFCompensation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCTFCompensation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCTFCompensation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCTFCompensation
+Options:
+ [-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)
+ [-whiteRaise WhiteNoiseRaising (0.1 ).as(Real ) ] :Optional :WhiteNoiseRaising(A)
+ [-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
+mode 2: x ctf, phase flipping and ctf-multiplying
+mode 3: x 1/ctf (0.1<|ctf| phase flipping and ctf-divided
+mode 4: x ctf/(SQR(ctf)+SQR(NS)) phase-flipping + Winner Filtering
+mode 5: x SQR(ctf) x ctf/|ctf| phase-flipping + ctf-Weighted
+mode 6: x 1/|ctf| (0.1<|ctf|) No phase-flipping + ctf-divided
+mode 7: x |ctf|/(SQR(ctf)+SQR(NS)) No phase flipping + Winner Filtering
+mode 8: x ctf /(SQR(ctf)+SQR(NS*exp(a*R))) phase flipping + Winner Filtering + NS-raising
+mode 9: x |ctf|/(SQR(ctf)+SQR(NS*exp(a*R))) No phase flipping + Winner Filtering + NS-raising
+----- Note -----
+You can enter information from -info
+Info file was made by llExtractWithLayerSeparationFilamentInfo -oI
+defocus Cs kV AmplitudeContrast
+----- Note1 -----
+-NoStig is the highest priority and so -Astig and parameters in -info2 are ignored.
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrcImageCTFCompensationForTiltImage: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCTFCompensationForTiltImage</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCTFCompensationForTiltImage</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCTFCompensationForTiltImage
+Options:
+ [-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>
+</HTML>
-/bin/bash: mrcImageColoring: そのようなファイルやディレクトリはありません
+dyld: Library not loaded: @rpath/libgif.dylib
+ Referenced from: /Applications/Eos/src/Tools/mrcImage/mrcImageColoring/src/mrcImageColoring
+ Reason: image not found
-/bin/bash: mrcImageCoreImageCalc: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageCoreImageCalc: No such file or directory
-/bin/bash: mrcImageCorrelationServer: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageCorrelationServer: No such file or directory
-/bin/bash: mrcImageCorrelationWithCTFCompensation: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageCorrelationWithCTFCompensation: No such file or directory
-/bin/bash: mrcImageCutAndSetInArray: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageCutAndSetInArray: No such file or directory
Options:
[-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
+ [-C[ontour] Contour (10 ).as(Real ) ] :Optional :ContourLevel: 10 1.482197e-323ach
[-log Log (NULL ).as(appendFile ) ] :Optional :OutputDataFile
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
-/bin/bash: mrcImageEdgeImageGet: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageEdgeImageGet: No such file or directory
-/bin/bash: mrcImageEnhancementWithFuzzySets: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageEnhancementWithFuzzySets: No such file or directory
-/bin/bash: mrcImageFFTLayerLineExtraction: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageFFTLayerLineExtraction</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFFTLayerLineExtraction</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFFTLayerLineExtraction
+Options:
+ [-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
+----------------------
+-I option is stronger than -dY option.
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrcImageFOMCalc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageFOMCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFOMCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFOMCalc
+Options:
+ [-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]
+mrc[1] weight[1]
+.....
+mrc[n-1] weight[n-1]
+This algorithm is originated from K. Yonekura for Layer Lines. Nature/SupplmentTable 2
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrcImageFOMCalc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageFOMCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFOMCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFOMCalc
+Options:
+ [-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]
+mrc[1] weight[1]
+.....
+mrc[n-1] weight[n-1]
+This algorithm is originated from K. Yonekura for Layer Lines. Nature/SupplmentTable 2
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrcImageFilamentSearch: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageFilamentSearch: No such file or directory
-/bin/bash: mrcImageFractalFrourierShellCorrelation: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageFractalFrourierShellCorrelation: No such file or directory
-/bin/bash: mrcImageHelicalConvolution: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageHelicalConvolution: No such file or directory
-/bin/bash: mrcImageMergeFFT: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageMergeFFT: No such file or directory
-/bin/bash: mrcImageMultiCTFCompensation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageMultiCTFCompensation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageMultiCTFCompensation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageMultiCTFCompensation
+Options:
+ [-i[nput] In (stdin ).as(inFileList ) ] :Essential :Input: filename ...
+ [-info2 CTF (stdin ).as(inFileList ) ] :Optional :InputFileList: the same order as the input: ctfinfo from Display2/ctfDisplay
+ [-o[utput] Out (stdout ).as(outFile ) ] :Essential :OutputDataFile(average file)
+ [-f[ft] fftOut (stdout ).as(outFile ) ] :Optional :OutputDataFile(averaged fft file)
+ [-W[hiteNoise] WhiteNoise (1.0 ).as(Real ) ] :Optional :
+ [-W[hiteNoise]R[aising]WhiteNoiseRaising (1.0 ).as(Real ) ] :Optional :Weight:W*exp(WR*R)
+ [-maxW[hiteNoise]R[aising]MaxWhiteNoise (1.0 ).as(Real ) ] :Optional :max(W*exp(WR*R),maxWhiteNoise)
+ [-Ndep[endent]W[hiteNoise]R[aising]NdependentWhiteNoise(1 ).as(Integer ) ] :Optional :W*exp(WR*R)/sqrt(N)
+ [-SinWin SinWinRmin (0.1 ).as(Real )
+ SinWinRmax (1.0 ).as(Real ) ] :Optional :Windowing by sine function from Rmin[/A] to Rmax[/A]
+ [-MaxIter[ation] MaxIter (10 ).as(Integer ) ] :Optional :Max Iteration
+ [-ctfMode CTFMode (1 ).as(Integer ) ] :Optional :CTFMode: refer to mrcImageCTFObservation
+ [-solventMode solventMode (0 ).as(Real ) ] :Optional :If solvent flatterning is used, NEED
+ [-solventSTD solventSTD (-1.0 ).as(Real ) ] :Optional :If solvent flatterning is used as mode=1, NEED
+ [-log[file] Log (stderr ).as(outFile ) ] :Optional :Log File Name
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- InputFileFormat -----
+filename0 deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
+filename1 deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
+.................
+
+----- Input: ctfinfo, with the same order as the input; from Display2/ctfDisplay -----
+filename0.ctfinfo
+filename1.ctfinfo
+.................
+
+mode: 0 : CTF-weighted compensation, CTF/(SQR(CTF) + (NS)^2)
+mode: +1 : Adding solvent-flattening process
+mode: +16: Without phase flipping, in case of images after phase only correction.
+ </PRE>
+</BODY>
+</HTML>
-/bin/bash: mrcImageMultiCTFDetermination: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageMultiCTFDetermination</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageMultiCTFDetermination</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageMultiCTFDetermination
+Options:
+ [-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>
+</BODY>
+</HTML>
-/bin/bash: mrcImageNLMeansFilter: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageNLMeansFilter: No such file or directory
-/bin/bash: mrcImagePanoramaCreate: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImagePanoramaCreate</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImagePanoramaCreate</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImagePanoramaCreate
+Options:
+ [-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>
+</BODY>
+</HTML>
-/bin/bash: mrcImagePeakSearch: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImagePeakSearch: No such file or directory
-/bin/bash: mrcImagePrint: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImagePrint: No such file or directory
-/bin/bash: mrcImagePrint3D: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImagePrint3D: No such file or directory
-/bin/bash: mrcImagePut3D: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImagePut3D: No such file or directory
-/bin/bash: mrcImageROIs: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageROIs</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageROIs</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageROIs
+Options:
+ [-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
+ [-PadMode PadMode (0 ).as(Integer ) ] :Optional :PadMode(refer to mrcImagePad)
+ [-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
+1: Bilinear
+2: CubicConvolution
+----- Information File Format -----
+Shape ShapeInfo1 ... [Additional AdditionalInfo1 ...]
+...............
+Shape: OutFileName Rect blx bly brx bry trx try tlx tly
+Shape: OutFileName TiltRect blx bly brx bry trx try tlx tly
+Shape: OutFileName Rect2 centerx centery width height
+Shape: OutFileName Circle centerx centery radius
+Shape: OutFileName Line startx starty endx endy
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrcImageSNEstimate: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageSNEstimate: No such file or directory
-/bin/bash: mrcImageShapePCA: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageShapePCA: No such file or directory
-/bin/bash: mrcImageShapePCAFit: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageShapePCAFit: No such file or directory
-/bin/bash: mrcImageShapeRelaxation: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageShapeRelaxation: No such file or directory
-/bin/bash: mrcImageShapeSearch: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageShapeSearch: No such file or directory
-/bin/bash: mrcImageSimilarityEstimate: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageSimilarityEstimate</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageSimilarityEstimate</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageSimilarityEstimate
+Options:
+ [-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*
+1: Phase Correlation FxG*/ |FxG*|
+2: Phase Correlation FxG*/sqrt(|FxG*|)
+3: Normalized Normal Correlation FxG*/|F||G|)
+16: (0,0) = 0
+ctfmode:1 (Phase and Amplitude)
+ctfinf format:defocus Cs kV AoverP
+</PRE>
+</BODY>
+</HTML>
-../../../../../hostdepend/X86MAC64//X86MAC64
\ No newline at end of file
+../../../../../hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageSoftEdge/src/X86MAC64
\ No newline at end of file
-/bin/bash: mrcImageSpatialFrequencyFilter: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageSpatialFrequencyFilter</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageSpatialFrequencyFilter</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageSpatialFrequencyFilter
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input: mrcImage
+ [-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::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
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-<HTML>
-<HEAD>
-<TITLE>mrcImageSphereCheck</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageSphereCheck</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageSphereCheck
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output:
- [-n[ormalized] OutNOr (NULL ).as(outFile ) ] :Optional :Output: NormalizedImage
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageSphereCheck: No such file or directory
[-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(%)
+ [-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
-/bin/bash: mrcImageTiltAxisSearchHelp: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageTiltAxisSearchHelp</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageTiltAxisSearchHelp</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageTiltAxisSearchHelp
+Options:
+ [-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>
+</BODY>
+</HTML>
-/bin/bash: mrcImageUnbentROI: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageUnbentROI: No such file or directory
-/bin/bash: mrcImageVarianceAnalysis: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageVarianceAnalysis</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageVarianceAnalysis</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageVarianceAnalysis
+Options:
+ [-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
+In1
+In2
+...
+>>>>> Within In1 etc. A + B*density
+filename1-1 A B
+.....
+---- Variance Analysis-----
+-- Algorithm
+ VarianceRatio := VarinceBetweenClasses/(SumOfVarianceWithinEachClass)
+ VarinceBetweenClasses: variance between classes
+ VarinceWithClasses: variance within each class
+
+
+ ---- General Information -----
+ Kai-distribution: Kai^2 = SumOf (Xi - AvgOfXi)^2/sigma^2
+ = s^2*(n-1)/sigma^2 : degree of freedom n-1
+ when variables Xi are due to N(u, sigma^2)
+ Kai-distribution: Kai^2 = Kai1^2 + Kai2^2 : degree of freedom m1 + m2
+ F-distribution: F = (Kai1^2/k1)/(Kai2^2/k2) : degree of freedom : (k1, k2)
+ (s1^2/sigma1^2)/(s2^2/sigma2^2) : degree of freedom : (k1-1, k2-1)
+ If sigma1 == sigma2, then
+ s1^2/s2^2 (Variance Ratio) : degree of freedom : (k1-1, k2-1)
+</PRE>
+</BODY>
+</HTML>
[-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%
+ 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
-/bin/bash: mrcView: そのようなファイルやディレクトリはありません
+/bin/bash: mrcView: No such file or directory
-/bin/bash: pdbAtomSection: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>pdbAtomSection</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbAtomSection</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbAtomSection
+Options:
+ [-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
+
+
+
+format for Flags File
+one line of the file
+chainIdertifier&sequenceNumber(R123) FlagMode circleRedius circlelinewidth fontsize
+FlagMode
+ 0: display nothing
+ 1: one char amino acid name
+ 2: three char amino acid name
+ 4: chain identifier
+ 8: sequence number
+ 16: display any atom
+ default: 13 (display R123T)
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbHomologySearch: そのようなファイルやディレクトリはありません
+/bin/bash: pdbHomologySearch: No such file or directory
-/bin/bash: pdbRhoFit: そのようなファイルやディレクトリはありません
+/bin/bash: pdbRhoFit: No such file or directory
-/bin/bash: pdbRhoFitTm: そのようなファイルやディレクトリはありません
+/bin/bash: pdbRhoFitTm: No such file or directory
-/bin/bash: pdbTempFactorSet: そのようなファイルやディレクトリはありません
+/bin/bash: pdbTempFactorSet: No such file or directory
-/bin/bash: pdbTrans: そのようなファイルやディレクトリはありません
+<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: pdbView: そのようなファイルやディレクトリはありません
+/bin/bash: pdbView: No such file or directory
-/bin/bash: mrcImageNeuralNetParticleExtraction: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageNeuralNetParticleExtraction: No such file or directory
-/bin/bash: mrcImageNeuralNetParticleLearning: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageNeuralNetParticleLearning</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageNeuralNetParticleLearning</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageNeuralNetParticleLearning
+Options:
+ [-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 ).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>
+</HTML>
-/bin/bash: CheckCommonLineData: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>CheckCommonLineData</TITLE>
+</HEAD>
+<BODY>
+<H1>CheckCommonLineData</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: CheckCommonLineData
+Options:
+ [-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>
+</HTML>
-/bin/bash: CheckOfOrientation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>CheckOfOrientation</TITLE>
+</HEAD>
+<BODY>
+<H1>CheckOfOrientation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: CheckOfOrientation
+Options:
+ [-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
+-ov : output Value data
+
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: CheckOrientationByDegree: そのようなファイルやディレクトリはありません
+/bin/bash: CheckOrientationByDegree: No such file or directory
-/bin/bash: CommonLineCalculation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>CommonLineCalculation</TITLE>
+</HEAD>
+<BODY>
+<H1>CommonLineCalculation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: CommonLineCalculation
+Options:
+ [-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
+ 1 : in 2004/09/23 (vector product)
+
+----- input file format -----
+-Im : 0
+RotationalMode1 angle1 angle2 angle3 RotationalMode2 angle1 angle2 angle3
+RotationalMode1 angle1 angle2 angle3 RotationalMode2 angle1 angle2 angle3
+ . . . . . . . .
+ . . . . . . . .
+ . . . . . . . .
+ . . . . . . . .
+ . . . . . . . .
+
+-Im : 1
+filename RotationalMode angle1 angle2 angle3
+ . . . . .
+ . . . . .
+ . . . . .
+ . . . . .
+ . . . . .
+
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: LCalculationForOrientationSearch: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>LCalculationForOrientationSearch</TITLE>
+</HEAD>
+<BODY>
+<H1>LCalculationForOrientationSearch</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: LCalculationForOrientationSearch
+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: ProjectionDirectionMapCreate: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>ProjectionDirectionMapCreate</TITLE>
+</HEAD>
+<BODY>
+<H1>ProjectionDirectionMapCreate</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ProjectionDirectionMapCreate
+Options:
+ [-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 .
+
+----- input file format -----
+filename rotationalmode angle angle angle
+ . . . . .
+ . . . . .
+ . . . . .
+ . . . . .
+
+----- mode -----
+-m : 0 : Not separate plus and minus of theta. Create one line data
+ 1 : separate plus and minus of theta. Create one line data
+ 2 : separate plus and minus of theta. Create two line data
+ 3 : Mollweide expressionn
+----- mode -----
+-Rm : 0 : Not change rotational mode
+ 1 : Change rotational mode to ZONS
+
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: WeightCalculationOfCommonLineSearch: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>WeightCalculationOfCommonLineSearch</TITLE>
+</HEAD>
+<BODY>
+<H1>WeightCalculationOfCommonLineSearch</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: WeightCalculationOfCommonLineSearch
+Options:
+ [-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 :
+ 0 : Addition weight
+ 1 : Multiplication weight
+
+----- input file format -----
+filename(sin) rotationalmode angle angle angle
+ . . . . .
+ . . . . .
+ . . . . .
+ . . . . .
+
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: WeightCalculationOfCommonLineSearchByAllSinogram: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>WeightCalculationOfCommonLineSearchByAllSinogram</TITLE>
+</HEAD>
+<BODY>
+<H1>WeightCalculationOfCommonLineSearchByAllSinogram</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: WeightCalculationOfCommonLineSearchByAllSinogram
+Options:
+ [-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
+ 2 : ued to Derivation1D Correlation
+ 4 : ued to Derivation2D Correlation
+ 8 : ued to Length Correlation
+ 15 : ued to All Correlation
+ (* inupt sum)
+
+
+----- mode -----
+-m : 0 : get memory of mrcImage
+ 1 : don't get memory of mrcImage
+
+</PRE>
+</BODY>
+</HTML>
-<HTML>
-<HEAD>
-<TITLE>calcCommonLine</TITLE>
-</HEAD>
-<BODY>
-<H1>calcCommonLine</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: calcCommonLine
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputEulerAnglesList
- [-R[ot]1 EMode1 (YOYS ).as(String )
- Rot1_1 (0.0 ).as(Real )
- Rot1_2 (0.0 ).as(Real )
- Rot1_3 (0.0 ).as(Real ) ] :Optional :Input: RotAngle1[degree]
- [-R[ot]2 EMode2 (YOYS ).as(String )
- Rot2_1 (0.0 ).as(Real )
- Rot2_2 (0.0 ).as(Real )
- Rot2_3 (0.0 ).as(Real ) ] :Optional :Input: RotAngle2[degree]
- [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output:Degrees
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: calcCommonLine: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>commonLinesSearchByVoting</TITLE>
-</HEAD>
-<BODY>
-<H1>commonLinesSearchByVoting</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: commonLinesSearchByVoting
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputCorrelationMapList
- [-i[nput]c[ommonLines]InC (NULL ).as(inFile ) ] :Optional :InputCommonLinesList
- [-i[nput]c[orrect]c[ommonLines]InCC (NULL ).as(inFile ) ] :Optional :InputCorrectCommonLinesList
- [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputFilteredCommonLinesList
- [-o[utput]a[ll] OutA (NULL ).as(outFile ) ] :Optional :OutputAllCommonLinesList
- [-o[utput]d[etecting]r[ate]OutDR (NULL ).as(outFile ) ] :Optional :OutputDetectingRate
- [-o[utput]d[etecting]r[ate]a[ll]OutDRA (NULL ).as(outFile ) ] :Optional :OutputDetectingRateALL
- [-o[utput]p[eaks]h[istgram]OutPH (NULL ).as(outFile ) ] :Optional :OutputPeaksHistgram
- [-e[stimation]n[umber]en (1 ).as(Integer ) ] :Optional :EstimationNumber
- [-th[resholdLevel] th (1 ).as(Integer ) ] :Optional :ThresholdLevel
- [-histgramCreate[Flag] ] :Optional :HistgramCreateFlag
- [-extend[VotingFlag] ] :Optional :ExtendVotingFlag
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-Common lines are filtered only top G*100/sqrt(N) %, where N is the number of projections.
--extend Option
- Execute extended voting.
--m Option
- 0: normal
- 1: self voting (each angle histgram peak is multiplyed by its correlation value)
--th Option
- :
- -1: G = 2^(-1)
- 0: G = 2^0
- 1: G = 2^1
- 2: G = 2^2
- :
--en Option
- Estimation number of common line in a map.
- Running time is proportional to this number.
- Default; 1: the largest value in a correlation map is detected as common line.
-MapList Format
- numOfProjection1 numOfProjection2 mapFileName
- : : :
-CLinesList Format
- numOfProjection1 numOfProjection2 [ degOfProjection1 degOfProjection2 degDiff cor ] mapFileName
- : : : : : : :
-Voting Algorithm by Amit Singer et al (2010),
-"Detecting consistent common lines in cryo-EM by voting " (doi:10.1016/j.jsb.2009.11.003)
-----------------------------
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: commonLinesSearchByVoting: No such file or directory
-/bin/bash: ll2ltlg: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>ll2ltlg</TITLE>
+</HEAD>
+<BODY>
+<H1>ll2ltlg</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ll2ltlg
+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
+ [-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]
+InFile [char*80]
+OutFile[char*80]
+InveseOfllDataSamplingSize[Angstrom] llMax llDataMuxiumResolution[Angstrom]
+ltlgDataSamplingSize[Angstrom] ltlgDataMaximumRadius[Angstrom]
+IList(mode)
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: llExtract: そのようなファイルやディレクトリはありません
+/bin/bash: llExtract: No such file or directory
-/bin/bash: llExtractWithLayerSeparation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>llExtractWithLayerSeparation</TITLE>
+</HEAD>
+<BODY>
+<H1>llExtractWithLayerSeparation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llExtractWithLayerSeparation
+Options:
+ [-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)
+>> -ctf option <<
+----- Mode -----
+ 0: |CTFi|/Sigma(SQR(CTFi))
+ 1: CTFi /Sigma(SQR(CTFi))
+>> If -ctf, the file list indicated by -i must include the below information
+filename weight defocus[A] Cs[mm] AccV[kV] ratioOfAmpToPhase mode
+>> llDataSepartionControlFile <<
+llMax(different)
+nl Z numberOfN n0 n1 n2...
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: llExtractWithLayerSeparationServer: そのようなファイルやディレクトリはありません
+/bin/bash: llExtractWithLayerSeparationServer: No such file or directory
-/bin/bash: llExtractWithLayerSeparationSingle: そのようなファイルやディレクトリはありません
+/bin/bash: llExtractWithLayerSeparationSingle: No such file or directory
-/bin/bash: ltlg2mrc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>ltlg2mrc</TITLE>
+</HEAD>
+<BODY>
+<H1>ltlg2mrc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ltlg2mrc
+Options:
+ [-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
+ defalt: 0
+Mode:
+
+
+If control file is used, control file fora filename to output
+
+InputFileName(char[72])A])
+Title(char[60])A])
+Y|N(char[1]) : No use
+deltaX[A](if Y)||deltaY[A](if N)(F10.5) : You need not care for deltaX or deltaY in this tool because deltaX = deltaY. You had better care for that for compatibility.
+C[A]rMax[A](2F7.0) : C[A]: Spacing of the 1st layer line in real space ; rMax: Maximum of radial elements.
+phiStart[degree](F7.0) : phi at Z = 0
+zMin[A],zMax[A],deltaz[A](3F7.0) : z-section parameters for(z=zMin; z<zMax; z+=deltaz)
+Weight(F7.0) : Weight of the 0th layer line
+NNL,WEIGHT(I2,F8.0) : IF(NNL==99 && NN(LL)!=NL(LL)) WT(LL) = 0.0; IF(NNL!=0 && NNL==NL(LL)) WT(LL) = WEIGHT and Repeat until NNL == 0 or 99 or None
+ACUT(F7.0) : IF(ACUT>Density[x][y]) Density[x][y]= 0.0
+Mean,Sigma(2F7.0) : Mean : Mean of hrzData?; Sigma : Standard Deviation of hrzData?
+OutputFile : hrz-data filename to output
+
+#### Attention ####
+ In using this tool, you need not keep promises about format(F7.0 etc.).
+Instead, you need separate numbers with more space than one.
+Usually compatible but you need care when numbers have a line with no space.
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: ltlg2ps: そのようなファイルやディレクトリはありません
+/bin/bash: ltlg2ps: No such file or directory
-/bin/bash: marker2Dto3DEstimator: そのようなファイルやディレクトリはありません
+/bin/bash: marker2Dto3DEstimator: No such file or directory
-/bin/bash: mrc2Dto3D: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrc2Dto3D</TITLE>
+</HEAD>
+<BODY>
+<H1>mrc2Dto3D</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrc2Dto3D
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputDataFile
+ [-I[nput] In2 (NULL ).as(inFileListNoOpen ) ] :Optional :InputDataFile
+ [-each ] :Optional :Read each projection file if necessary, not at once.
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-O[utput] Out2 (NULL ).as(outFile ) ] :Optional :OutputDataFile[2DMulti]
+ [-Rmax Rmax (1.0 ).as(Real ) ] :Optional :Rmax: High Cut [/A]
+ [-single single (1 ).as(Integer ) ] :Optional :SingleTiltMode
+ [-singleFilter singleFilter (0 ).as(Integer ) ] :Optional :SingleFilterMode
+ [-InterpolationMode InterpolationMode (1 ).as(Integer ) ] :Optional :InterpolationMode
+ [-Double ] :Optional :DoubleTiltMode
+ [-DoubleCounter DoubleCounter (NULL ).as(outFile ) ] :Optional :DoubleCounter
+ [-CounterThreshold CounterThreshold (1e-6 ).as(Real ) ] :Optional :CounterThreshold
+ [-CounterThresholdModeCounterThresholdMode(0 ).as(Integer ) ] :Optional :CounterThresholdMode
+ [-WeightMode WeightMode (0 ).as(Integer ) ] :Optional :WeightMode
+ [-thicknessWeight ] :Optional :ThicknessWeight
+ [-Sub[Sampling] SubSampling (1 ).as(Integer ) ] :Optional :SubSampling: [pixel]
+ [-PlusXrot ] :Optional :plus x-rotation by 180 for rasmol.
+ [-N Nx (0 ).as(Integer )
+ Ny (0 ).as(Integer )
+ Nz (0 ).as(Integer ) ] :Optional :OutputSize
+ [-SIRT ] :Optional :by SIRT
+ [-max[Iter] maxIter (30 ).as(Integer ) ] :Optional :MaxIteration for SIRT
+ [-rms rms (1.0 ).as(Real ) ] :Optional :Ending Conditions: rms for SIRT
+ [-CTF[Info] CTFInfo (NULL ).as(inFileList ) ] :Optional :CTFInfo: for SIRT
+ [-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 -----
+-m Option
+ 0:SimpleBackProjection
+ 1:FilteredBackProjection(Fourier Space)
+ 2:WeightedBackProjection(Real Space)
+-single 0|1
+ 0: tilt axis is parallel to x-axis
+ 1: tilt axis is parallel to y-axis
+-singleFilter 0|1|2
+ 0: simple rho filter
+ 1: Ram-Lak Filter
+ 2: Shepp-Logan Filter
+-Double
+ Double Tilt
+-WeightMode
+ 1 : RealSpace: Circle(same density)
+ 2 : RealSpace: Circle(weighted density)
+ 3 : RealSpace: Square(weighted density)
+ 4 : Fourier Space : Plane(same density) -CounterThreshold 0.5
+ 5 : Fourier Space : Plane(Linear Gradient)-CounterThreshold 0.5
+ 6 : Fourier Space : Plane(Cosine Gradient) Current Recommende using -CounterThreshold 0.5
+-------------------------------
+-I Option file format
+filename0 RotationOrder0 rot1 rot2 rot3
+filename1 RotationOrder1 rot1 rot2 rot3
+.......................................
+>>> RotationOrder : Eular Angle Expression <<<
+Example: YOYS : RotY(rot3)RotX(rot2)RotY(rot1)*v
+First Rotation : y-axis : Y: Y : [X|Y|Z] Axis used initially
+Second Rotation : x-axis : O: Odd : [O|E] Parity of axis permutation
+Last Rotation : z-axis : Y: Yes : [Y|N] Repetition of initial axis as last
+v1 = A v0 : S: Staic : [S|R] Frame from which axes are taken
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrc2Dto3DforVariation: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2Dto3DforVariation: No such file or directory
-/bin/bash: mrcImageOrientationSearch: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageOrientationSearch: No such file or directory
-/bin/bash: mrcImageOrientationSearchByHigherSelection: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageOrientationSearchByHigherSelection</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageOrientationSearchByHigherSelection</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageOrientationSearchByHigherSelection
+Options:
+ [-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>
+</BODY>
+</HTML>
-/bin/bash: mrcImageOrientationSearchByHybridization: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageOrientationSearchByHybridization</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageOrientationSearchByHybridization</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageOrientationSearchByHybridization
+Options:
+ [-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
+
+----- IncreaseRate -----
+-ir : 1 >> Increase number is 45 (filenum = 10)
+ 2 >> Increase number is 90 (filenum = 10)
+
+----- HybridizationPointNumber -----
+-hpn : The number of hybridization points
+
+----- Mode of selection -----
+-ms : 0 : random
+ 1 : myself (-ird)
+
+----- Mode -----
+-m : 0 : create children angle file
+ 1 : do not create children angle file , create match angle file
+
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrcImageOrientationSearchBySimultaneousMinimization: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageOrientationSearchBySimultaneousMinimization</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageOrientationSearchBySimultaneousMinimization</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageOrientationSearchBySimultaneousMinimization
+Options:
+ [-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
+ : 1 : myself (-ird)
+
+----- Mode --------------
+-m : 0 : input data --> sinogram
+ : 1 : --> sinogramFT
+
+----- Angle -------------
+-dt : DEGREE
+-dp : DEGREE
+-pdt : DEGREE
+-pdp : DEGREE
+
+----- ModeOfInitialData -------------
+-mid : 0 : There is not initial data
+ 1 : There is initial data (-iid)
+
+----- ModeOfLcalculation -------------
+-mL : 0 : differential of length
+ 1 : differential of phase
+ 2 : addition to derivation1D (multiply)
+ 3 : addition to derivation1D (difference)
+
+----- ModeOfThresholdAngularWeight -------------
+-mTA : 0 : 1.0e-4
+ 1 : 1 degree
+ 2 : dpsi
+
+----- ModeOfStartPoint -------------
+-msp : 0 : origin
+ 1 : initial data (-iid)
+
+----- ModeOfAngularArea -------------
+-maa : 0 : all area
+ 1 : aroud previous delta (-pdt -pdp)
+
+----- ModeOfCalculationArea -------------
+-mca : 0 : all area
+ 1 : cut under -tca(1/angstrom)
+
+----- ModeOfFix -------------
+-mf : 0 : don't fix one plane
+ 1 : fix one plane (first file is fixed)
+
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrcRadon2Dto3D: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcRadon2Dto3D</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcRadon2Dto3D</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcRadon2Dto3D
+Options:
+ [-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
+ 1 = HigherOrder (-T)
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: energyTransferModelCheck: そのようなファイルやディレクトリはありません
+<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>
-/bin/bash: muscleSimulation: そのようなファイルやディレクトリはありません
+/bin/bash: muscleSimulation: No such file or directory
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