+++ /dev/null
-SOURCE=\
-Integration \
-PrevReleased \
-backup \
-bin \
-data \
-database \
-distribute \
-env \
-hostdepend \
-include \
-lib \
-optional \
-others \
-others2 \
-pione \
-sbin \
-src \
-tutorial \
-util \
-zephyr \
-#LastSource
+++ /dev/null
-SOURCE=\
-Integration \
-PrevReleased \
-backup \
-bin \
-data \
-database \
-distribute \
-env \
-hostdepend \
-include \
-lib \
-optional \
-others \
-others2 \
-pione \
-sbin \
-src \
-tutorial \
-util \
-zephyr \
-#LastSource
--- /dev/null
+../sbin/MachineIndependent
\ No newline at end of file
--- /dev/null
+../sbin/MachineIndependent
\ No newline at end of file
set auto_index(menuMultiRoiAllDeleteCommand) [list source [file join $dir Display2MenuROI.wish]]
set auto_index(menuMultiRoiDeleteCommand) [list source [file join $dir Display2MenuROI.wish]]
set auto_index(menuEditCreate) [list source [file join $dir Display2MenuROI.wish]]
-set auto_index(fft2dCmd) [list source [file join $dir fft2dCmd.wish]]
set auto_index(layerLineRecreate) [list source [file join $dir LayerLineUtil.wish]]
set auto_index(layerLineCreate) [list source [file join $dir LayerLineUtil.wish]]
set auto_index(layerLineClear) [list source [file join $dir LayerLineUtil.wish]]
set auto_index(sectionClear) [list source [file join $dir SectionUtil.wish]]
set auto_index(sectionChange) [list source [file join $dir SectionUtil.wish]]
set auto_index(unitCellRecreate) [list source [file join $dir UnitCell.wish]]
+set auto_index(fft2dCmd) [list source [file join $dir fft2dCmd.wish]]
char seperator[4];
dmFileInteger4 ninfo;
dmFileInteger4* info;
+ long pValue; // Offset
void* value; // Array or value
void** value2; // Struct
void** value3; // Array of Struct
char seperator[4];
dmFileInteger8 ninfo;
dmFileInteger8* info;
+ long pValue;
void* value; // Array or value
void** value2; // Struct
void** value3; // Array of Struct
--- /dev/null
+#ifndef EOS_BAYES_H
+#define EOS_BAYES_H
+
+typedef struct eosBayesDistribution {
+ float min;
+ float max;
+ float delta;
+ int n;
+ float* prob;
+} eosBayesDistribution;
+
+
+typedef struct eosBayes {
+ int numDistribution;
+ eosBayesDistribution* prior;
+ eosBayesDistribution* posterior;
+
+ int numLikelihood;
+ eosBayesDistribution* likelihood;
+} eosBayes;
+
+
+#endif /* EOS_BAYES_H */
float Cx;
float Cy;
int flagAverage;
+ int flagAzimuth;
+ int NAzimuth;
+ floatVector* azimuth;
} lmrcImageRadialDistributionInfo;
/* struct end */
char seperator[4];
dmFileInteger4 ninfo;
dmFileInteger4* info;
+ long pValue; // Offset
void* value; // Array or value
void** value2; // Struct
void** value3; // Array of Struct
char seperator[4];
dmFileInteger8 ninfo;
dmFileInteger8* info;
+ long pValue;
void* value; // Array or value
void** value2; // Struct
void** value3; // Array of Struct
static char __sccs_id[] = "@(#)mrcImageCopy ver1.1; Date:96/05/08 @(#)";
#include <math.h>
#include <stdlib.h>
+#define DEBUG
+#include "genUtil.h"
#include "../inc/mrcImage.h"
void
mrcImageParaTypeInteger x, y, z;
int k;
- for(iz=0; iz<dst->HeaderN.z; iz++) {
- for(iy=0; iy<dst->HeaderN.y; iy++) {
- for(ix=0; ix<dst->HeaderN.x; ix++) {
- x = (int)(ix - to.x + 0.5);
- y = (int)(iy - to.y + 0.5);
- z = (int)(iz - to.z + 0.5);
- mrcPixelDataGet(src, x, y, z, &data, mrcPixelRePart, mrcPixelHowNearest);
- mrcPixelDataSet(dst, ix, iy, iz, data, mrcPixelRePart);
+ DEBUGPRINT3("to: %g %g %g in lmrcImageCopy\n", to.x, to.y, to.z);
+ DEBUGPRINT3("src: %d %d %d in lmrcImageCopy\n", src->HeaderN.x, src->HeaderN.y, src->HeaderN.z);
+ DEBUGPRINT3("dst: %d %d %d in lmrcImageCopy\n", dst->HeaderN.x, dst->HeaderN.y, dst->HeaderN.z);
+ for(iz=0; iz<src->HeaderN.z; iz++) {
+ for(iy=0; iy<src->HeaderN.y; iy++) {
+ for(ix=0; ix<src->HeaderN.x; ix++) {
+ x = (int)(ix + to.x + 0.5);
+ y = (int)(iy + to.y + 0.5);
+ z = (int)(iz + to.z + 0.5);
+ mrcPixelDataGet(src, ix, iy, iz, &data, mrcPixelRePart, mrcPixelHowNearest);
+ mrcPixelDataSet(dst, x, y, z, data, mrcPixelRePart);
}
}
}
pdbFileParaTypeInteger
pdbZValueGet(pdbFile* pdb)
{
- if( pdb->PDB->AtomName[1] == 'H') {
- return 1;
- } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'C') {
- return 6;
- } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'N') {
- return 7;
- } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'O') {
- return 8;
- } else if(pdb->PDB->AtomName[0] == 'M' && pdb->PDB->AtomName[1] == 'G') {
- return 12;
- } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'P') {
- return 15;
- } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'S') {
- return 16;
+ if( pdb->PDB->Footnote[6] == ' ' && pdb->PDB->Footnote[7] == 'H') {
+ return 1;
+ } else if(pdb->PDB->Footnote[6] == ' ' && pdb->PDB->Footnote[7] == 'C') {
+ return 6;
+ } else if(pdb->PDB->Footnote[6] == ' ' && pdb->PDB->Footnote[7] == 'N') {
+ return 7;
+ } else if(pdb->PDB->Footnote[6] == ' ' && pdb->PDB->Footnote[7] == 'O') {
+ return 8;
+ } else if(pdb->PDB->Footnote[6] == 'N' && pdb->PDB->Footnote[7] == 'A') {
+ return 11;
+ } else if(pdb->PDB->Footnote[6] == 'M' && pdb->PDB->Footnote[7] == 'G') {
+ return 12;
+ } else if(pdb->PDB->Footnote[6] == ' ' && pdb->PDB->Footnote[7] == 'P') {
+ return 15;
+ } else if(pdb->PDB->Footnote[6] == ' ' && pdb->PDB->Footnote[7] == 'S') {
+ return 16;
+ } else if(pdb->PDB->Footnote[6] == 'C' && pdb->PDB->Footnote[7] == 'L') {
+ return 17;
+ } else if(pdb->PDB->Footnote[6] == ' ' && pdb->PDB->Footnote[7] == 'K') {
+ return 19;
+ } else if(pdb->PDB->Footnote[6] == 'C' && pdb->PDB->Footnote[7] == 'A') {
+ return 20;
+ } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'H') {
+ return 1;
+ } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'C') {
+ return 6;
+ } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'N') {
+ return 7;
+ } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'O') {
+ return 8;
+ } else if(pdb->PDB->AtomName[0] == 'N' && pdb->PDB->AtomName[1] == 'A') {
+ return 11;
+ } else if(pdb->PDB->AtomName[0] == 'M' && pdb->PDB->AtomName[1] == 'G') {
+ return 12;
+ } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'P') {
+ return 15;
+ } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'S') {
+ return 16;
} else if(pdb->PDB->AtomName[0] == 'C' && pdb->PDB->AtomName[1] == 'L') {
return 17;
- } else if(pdb->PDB->AtomName[0] == 'C' && pdb->PDB->AtomName[1] == 'A') {
- return 20;
+ } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'K') {
+ return 19;
+ } else if(pdb->PDB->AtomName[0] == 'C' && pdb->PDB->AtomName[1] == 'A') {
+ return 20;
} else if(pdb->PDB->AtomName[0] == 'F' && pdb->PDB->AtomName[1] == 'E') {
return 26;
- } else {
- fprintf(stderr, "Not supported element: %c%c to Carbon\n", pdb->PDB->AtomName[0], pdb->PDB->AtomName[1]);
- return 6;
- }
+ } else {
+ fprintf(stderr, "Not supported element: %c%c\n", pdb->PDB->Footnote[6], pdb->PDB->Footnote[7]);
+ fprintf(stderr, "Not supported element: %c%c\n", pdb->PDB->AtomName[0], pdb->PDB->AtomName[1]);
+ return 6;
+ }
+ return 6;
}
String \
Vector \
dummy \
+eosBayes \
eosCuda \
eosFunc \
eosList \
String \
Vector \
dummy \
+eosBayes \
eosCuda \
eosFunc \
eosList \
--- /dev/null
+SOURCE=\
+doc \
+inc \
+src \
+#LastSource
--- /dev/null
+SOURCE=\
+doc \
+inc \
+src \
+#LastSource
Cluster \
Coord \
DCDFile \
+DataManip \
Integration \
admin \
array \
Cluster \
Coord \
DCDFile \
-DataManip \
Integration \
admin \
array \
+++ /dev/null
-SOURCE=\
-clusterLog2ToLog \
-clusterLogASCII2Binary \
-clusterShow \
-#LastSource
+++ /dev/null
-SOURCE=\
-coordRotation \
-pointsSetToPDB \
-#LastSource
+++ /dev/null
-SOURCE=\
-dcdAtomChangeDistanceFromAtom \
-dcdAtomDistanceDistribution \
-dcdCompareCA \
-dcdDistanceAtomBetweenAtom \
-dcdFilePrint \
-dcdInfo \
-dcdSelectAtoms \
-dcdSerectAtom \
-dcdTimeSeriesBehavior \
-#LastSource
--- /dev/null
+SOURCE=\
+bmp2mrc \
+dm \
+#LastSource
--- /dev/null
+include ../../Config/Define.inc
+include ../Config/Define.inc
+include Config/Define.inc
+include .Source
+
+all:
+ for dir in ${SOURCE} ; \
+ do \
+ if [ -d $${dir} ] ; then \
+ $(CD) $${dir}; make all; $(CD) ..; \
+ fi \
+ done
+
+install:
+ for dir in ${SOURCE} ; \
+ do \
+ if [ -d $${dir} ] ; then \
+ $(CD) $${dir}; make install; $(CD) ..; \
+ fi \
+ done
+
+put:
+ for dir in ${SOURCE} ; \
+ do \
+ if [ -d $${dir} ] ; then \
+ $(CD) $${dir}; make put; $(CD) ..; \
+ fi \
+ done
+
+putSF:
+ if [ -f private ] ; then \
+ echo "$(WORLDNAME)/$(CLASSNAME) is private " ; \
+ else \
+ for dir in ${SOURCE} ; \
+ do \
+ if [ -d $${dir} ] ; then \
+ $(CD) $${dir}; make putSF; $(CD) ..; \
+ fi \
+ done \
+ fi
+
+clean:
+ for dir in ${SOURCE} ; \
+ do \
+ $(CD) $${dir}; make clean; $(CD) ..; \
+ done
+
+check:
+ @for dir in ${SOURCE} ; do \
+ if [ -d $${dir} ] ; then \
+ $(CD) $${dir}; \
+ echo $${dir}; \
+ $(RM) Makefile; \
+ $(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/Makefile Makefile ; \
+ make check; \
+ $(CD) ..; \
+ fi \
+ done
+
+update:
+ @for dir in ${SOURCE} ; do \
+ if [ -d $${dir} ] ; then \
+ $(CD) $${dir}; \
+ echo $${dir}; \
+ $(RM) Makefile; \
+ $(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/Makefile Makefile ; \
+ make update; \
+ $(CD) ..; \
+ fi \
+ done
+
+depend: check
+ @for dir in ${SOURCE} ; \
+ do \
+ $(CD) $${dir}; make depend; $(CD) ..; \
+ done
+
+backup:
+ cd ../../..; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
+ tar uvf ${EOS_HOME}/backup/EosBase.tar .[A-z]*
+ @for dir in ${SOURCE} ; \
+ do \
+ $(CD) $${dir}; make backup; $(CD) ..; \
+ done
+
+backup-all:
+ cd ../../..; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
+ tar rvf ${EOS_HOME}/backup/EosBase.tar .[A-z]*
+ @for dir in ${SOURCE} ; \
+ do \
+ $(CD) $${dir}; make backup; $(CD) ..; \
+ done
+
+distribute:
+ cd ../../..; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
+ @for dir in ${SOURCE} ; \
+ do \
+ $(CD) $${dir}; make distribute; $(CD) ..; \
+ done
+
+distribute-all:
+ cd ../../..; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
+ @for dir in ${SOURCE} ; \
+ do \
+ $(CD) $${dir}; make distribute-all; $(CD) ..; \
+ done
+
+++ /dev/null
-/Users/tacyas/Eos/src/Config/Template/ToolsHomeTemplate.Dir/Makefile
\ No newline at end of file
--- /dev/null
+include ../Config/Define.inc
+include Config/Define.inc
+include .Source
+
+include Config/Target.inc
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImage3DPeakGet</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImage3DPeakGet</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImage3DPeakGet
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:3D
+ [-I[nformation] Info (stdin ).as(inFile::ASCII ) ] :Optional :Input:ROI Info
+ [-o[utput] Out (stdout ).as(outFile::ASCII ) ] :Optional :Output:Positon
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
<PRE>
Usage: mrcImageAutoCorrelationWithWindowing
Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
- [-O[utput] OutWin (NULL ).as(outFile ) ] :Optional :Output WindowedFile
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output
+ [-o[utput]c[entre] OutCentre (NULL ).as(outFile::mrcImage ) ] :Optional :OutputDataFile
+ [-O[utput] OutWin (NULL ).as(outFile::mrcImage ) ] :Optional :Output WindowedFile
[-W[indowing]y Wy (6 ).as(Real ) ] :Optional :Window Height: N.y * 1/Wy
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
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 6.950489e-310ach
+ [-C[ontour] Contour (10 ).as(Real ) ] :Optional :ContourLevel: 10 5.533535e-322ach
[-log Log (NULL ).as(appendFile ) ] :Optional :OutputDataFile
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
--- /dev/null
+/bin/bash: mrcImageSNEstimate: No such file or directory
(info.mode&HowToCreateImageBit));
for(iy=0; iy < info.rotny; iy+= droty) {
DEBUGPRINT2("%g %g\n", ix, iy);
+
+#ifdef DEBUG
+ {
+ pdbFileTop(&pdb);
+ pdbFileNextAtom(&pdb);
+ DEBUGPRINT3("(x, y, z)=(%g, %g %g)\n", pdb.PDB->Coord.x, pdb.PDB->Coord.y, pdb.PDB->Coord.z);
+ }
+#endif
+
if(!info.flagRotMode) {
roty = ((double)iy)/info.rotny*2.0*M_PI;
pdbRotationZXY(&pdb, rotx, -roty, -rotz);
pdbRotationFollowingEulerAngle(&pdb, info.RotMode, -roty, rotx, -rotz);
}
+#ifdef DEBUG
+ {
+ pdbFileTop(&pdb);
+ pdbFileNextAtom(&pdb);
+ DEBUGPRINT3("(x, y, z)=(%g, %g %g)\n", pdb.PDB->Coord.x, pdb.PDB->Coord.y, pdb.PDB->Coord.z);
+ }
+#endif
+
DEBUGPRINT3("rot: (%g %g %g) \n", rotx*DEGREE, roty*DEGREE, rotz*DEGREE);
+
lpdb2mrc2d(&mrc, &pdb, &linfo, 'z', 0);
+#ifdef DEBUG
+ {
+ char s[1024];
+
+ sprintf(s, "/tmp/test.mrc.%03d", (int)zsection);
+
+ mrcFileWrite(&mrc, s, "tmp", 0);
+ }
+#endif
if(!info.flagRotMode) {
pdbRotationYXZ(&pdb, -rotx, roty, rotz);
to.y = fmod(to.y*info.ny, out.HeaderN.y);
DEBUGPRINT2("map %f %f\n", to.x, to.y);
to.z = 0.0;
+ DEBUGPRINT3("to: %f %f %f\n", to.x, to.y, to.z);
lmrcImageCopy(&out, &mrc, to);
+#ifdef DEBUG
+ {
+ char s[1024];
+ sprintf(s, "/tmp/test.2d.%03d", (int)zsection);
+ mrcFileWrite(&out, s, "tmp", 0);
+ }
+#endif
}
if(info.flagOut3D) {
to.x = 0.0;
out3D.Tailer[(int)zsection].Cont.Rot1 = -roty;
out3D.Tailer[(int)zsection].Cont.Rot2 = rotx;
out3D.Tailer[(int)zsection].Cont.Rot3 = -rotz;
+ DEBUGPRINT3("to: %f %f %f\n", to.x, to.y, to.z);
lmrcImageCopy(&out3D, &mrc, to);
zsection += 1.0;
}
[-w[eight] Weight (1.0 ).as(Real ) ] :Optional :weight
[-sig[ma] Sigma (0.0 ).as(Real ) ] :Optional :Sigma[A]:Atom radius
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-cuda cudaDeviceID (0 ).as(Integer ) ] :Optional :UseCuda
[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode: 0 Merc; 1: Earth
----- Attention1 -----
If both of -s and -startEA, first -s and second -startEA will be performed
exec2:
@echo "----- Execution Check -----"
- ../$(OSTYPE)/$(OBJECTNAME) -i data/121p.shift.pdb -o data/121p.mrc2d2 -O data/121p.mrc2dStack2 -s -32 -32 -n 32 32 -d 2 2 -Rot 12 12 -m 1 -sig 3
+ ../$(OSTYPE)/$(OBJECTNAME) -i data/121p.shift.pdb -o data/121p.mrc2d2 -O data/121p.mrc2dStack2 -s -32 -32 -n 32 32 -d 2 2 -Rot 12 12 -m 3 -sig 3
+ @echo "----- Calc check -----"
+
+exec3:
+ @echo "----- Execution Check -----"
+ ../$(OSTYPE)/$(OBJECTNAME) -i data/121p.shift.pdb -o data/121p.mrc2d3 -O data/121p.mrc2dStack3 -s -32 -32 -n 32 32 -d 2 2 -Rot 4 4 -m 3 -sig 3
@echo "----- Calc check -----"
clean:
* * pdbZValueGet
* * return value: Atomic Mass of the current atom
*/
+/*
int
pdbZValueGet(pdbRecord* current)
{
}
return 1;
}
-
+*/
void
lpdb2mrc2dWithCTF(mrcImage* out, pdbFile* pdb, lpdb2mrc2dWithCTFInfo* linfo, ctfInfo* ctf, int mode)
{
if(i%100==0) {
fprintf(stderr, "%d\n", i);
}
- Z = pdbZValueGet(pdb->PDB);
+ Z = pdbZValueGet(pdb);
R = aH *pow(Z, -1.0/3.0);
mrcInit(&sub, NULL);
}
}
}
-
-/bin/bash: pdb2mrc2dWithCTF: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdb2mrc2dWithCTF</TITLE>
+</HEAD>
+<BODY>
+<H1>pdb2mrc2dWithCTF</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdb2mrc2dWithCTF
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: PDB
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: MRC
+ [-N Nx (2048 ).as(Integer )
+ Ny (2048 ).as(Integer ) ] :Optional :Input: Nx Ny [pixel]
+ [-d dx (1.72 ).as(Real )
+ dy (1.72 ).as(Real ) ] :Optional :Input: dx dy [A]
+ [-Centre cx (0 ).as(Real )
+ cy (0 ).as(Real )
+ cz (0 ).as(Real ) ] :Optional :Input: CentreX CentreY [A]
+ [-n nx (64 ).as(Integer )
+ ny (64 ).as(Integer ) ] :Optional :Input: nx ny for subimage [pixel]
+ [-kV kV (200. ).as(Real ) ] :Optional :kV
+ [-Cs Cs (1.7 ).as(Real ) ] :Optional :Cs
+ [-d[e]f[ocus] Defocus (10000 ).as(Real ) ] :Optional :Defocus [A] at z = 0
+ [-A[overP] AoverP (0.07 ).as(Real ) ] :Optional :AoverP
+ [-Ain Ain (0.2 ).as(Real ) ] :Optional :Beta: IlluminationAngle [mrad]
+ [-ctfMode ctfMode (33 ).as(Integer ) ] :Optional :ctfMode
+ [-E[uler]A[ngle] EulerAngle (XEYS ).as(String )
+ Rot1 (0 ).as(Real )
+ Rot2 (0 ).as(Real )
+ Rot3 (0 ).as(Real ) ] :Optional :EulerAngle: [degree]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
exec:
@echo "----- Execution Check -----"
- ../$(OSTYPE)/$(OBJECTNAME)
+ ../$(OSTYPE)/$(OBJECTNAME) -i data/121p.pdb -o data/121p.mrc
@echo "----- Calc check -----"
clean:
-/bin/bash: pdbCrystalCreate: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbCrystalCreate</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbCrystalCreate</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbCrystalCreate
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input:PDB
+ [-I[nfo] Info (NULL ).as(inFile ) ] :Essential :Input:Crystal Information
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output:PDB
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+----- CrystalInfo -----
+aAxis %15.6g %15.6g %15.6g
+bAxis %15.6g %15.6g %15.6g
+cAxis %15.6g %15.6g %15.6g
+CellLength %15.6g %15.6g %15.6g
+Origin %15.6g %15.6g %15.6g
+N %15d %15d %15d
+StartN %15d %15d %15d
+SpaceGroup %15d
+HelixInfo %10d %10d %10d
+### Attention ###
+Parameter Order is important: Dependent between CellLength and a|b|cAxis.
+ Because each of aAxis, bAxis, cAxis must be a unit vector.
+HelixInfo t u n
+----- CrystalSpaceGroup -----
+ 0 P1
+ 1 HelicalSymmmetry
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbHelix: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbHelix</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbHelix</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbHelix
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-3[D] Out3D (NULL ).as(outFile ) ] :Optional :OutputDataFile(3D-mrc)
+ [-2[D] Out2D (NULL ).as(outFile ) ] :Optional :OutputDataFile(2D-mrc projection(y-z))
+ [-d[elta] delta (5 ).as(Real ) ] :Optional :delta[A](mrc-file)
+ [-p[delphi] delphi (165 ).as(Real ) ] :Essential :deltaPhi
+ [-dp[delphi] deldelphi (5 ).as(Real ) ] :Optional :deltaDeltaPhi
+ [-z[deltaz] delz (5 ).as(Real ) ] :Essential :deltaz
+ [-n[Molecule] nMolecule (1 ).as(Integer ) ] :Essential :NumberOfMolecules
+ [-nx nx (1 ).as(Integer ) ] :Optional :Pixel[Def:]
+ [-ny ny (1 ).as(Integer ) ] :Optional :Pixel[Def:]
+ [-nz nz (1 ).as(Integer ) ] :Optional :Pixel[Def:]
+ [-Sx[tart] Startx (0.0 ).as(Real ) ] :Optional :Startx[A]
+ [-Sy[tart] Starty (0.0 ).as(Real ) ] :Optional :Starty[A]
+ [-Sz[tart] Startz (0.0 ).as(Real ) ] :Optional :Startz[A]
+ [-w[eight] Weight (1.0 ).as(Real ) ] :Optional :Weight
+ [-dx dx (2.5 ).as(Real ) ] :Optional :dx
+ [-dy dy (2.5 ).as(Real ) ] :Optional :dy
+ [-dz dz (2.5 ).as(Real ) ] :Optional :dz
+ [-startn startn (0 ).as(Integer ) ] :Optional :start molecule's index
+ [-startC startID (A ).as(Character ) ] :Optional :start chain ID
+ [-deltaSeq deltaSeq (1000 ).as(Integer ) ] :Optional :start chain ID
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbMove: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbMove</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbMove</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbMove
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-x X (0.0 ).as(Real ) ] :Optional :Move X[A]
+ [-y Y (0.0 ).as(Real ) ] :Optional :Move Y[A]
+ [-z Z (0.0 ).as(Real ) ] :Optional :Move Z[A]
+ [-originTo toX (0.0 ).as(Real )
+ toY (0.0 ).as(Real )
+ toZ (0.0 ).as(Real ) ] :Optional :move (0,0,0) to (X,Y,Z)
+ [-toOrigin fromX (0.0 ).as(Real )
+ fromY (0.0 ).as(Real )
+ fromZ (0.0 ).as(Real ) ] :Optional :move (X,Y,Z) to (0,0,0)
+ [-GCtoOrigin ] :Optional :GC(Gravity Centre) to origin
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbRhoFit: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbRhoFit</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbRhoFit</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbRhoFit
+Options:
+ [-i[nput]pdb[File] InPdb (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i[nput]mrc[File] InMrc (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput of ]mrc OutMrc (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-o[utput of ]txt OutTxt (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-o[utput of ]par OutPar (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-o[utput of ]pdb OutPDB (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-xmin xmin (0 ).as(Real ) ] :Optional :xmin for fitting
+ [-xmax xmax (0 ).as(Real ) ] :Optional :xmax for fitting
+ [-xd[elta] xDelta (1 ).as(Real ) ] :Optional :delta x for fitting
+ [-ymin ymin (0 ).as(Real ) ] :Optional :ymin for fitting
+ [-ymax ymax (0 ).as(Real ) ] :Optional :ymax for fitting
+ [-yd[elta] yDelta (1 ).as(Real ) ] :Optional :delta y for fitting
+ [-zmin zmin (0 ).as(Real ) ] :Optional :zmin for fitting
+ [-zmax zmax (82 ).as(Real ) ] :Optional :zmax for fitting
+ [-zd[elta] zDelta (1 ).as(Real ) ] :Optional :delta z for fitting
+ [-E[uler]A[ngle] EulerAngle (ZOYS ).as(String ) ] :Optional :Euler Angle for three-angle
+ [-phimin phimin (0 ).as(Real ) ] :Optional :phimin for fitting(degree)
+ [-phimax phimax (194 ).as(Real ) ] :Optional :phimax for fitting(degree)
+ [-phid[elta] phiDelta (2 ).as(Real ) ] :Optional :delta phi for fitting(degree)
+ [-psimin psimin (0 ).as(Real ) ] :Optional :psimin for fitting(degree)
+ [-psimax psimax (0 ).as(Real ) ] :Optional :psimax for fitting(degree)
+ [-psid[elta] psiDelta (2 ).as(Real ) ] :Optional :delta psi for fitting(degree)
+ [-thetamin thetamin (0 ).as(Real ) ] :Optional :thetamin for fitting(degree)
+ [-thetamax thetamax (0 ).as(Real ) ] :Optional :thetamax for fitting(degree)
+ [-thetad[elta] thetaDelta (2 ).as(Real ) ] :Optional :delta theta for fitting(degree)
+ [-n[ormalize]w[eight]normalizeWeight (100000000.0).as(Real ) ] :Optional :weight for normalize
+ [-n[ormalize]C[ontour]normalizeContour (0.0 ).as(Real ) ] :Optional :Contour Level for Normalize
+ [-I[nverse] ] :Optional :Black is High Density.
+ [-Zminus ] :Optional :Shift to -z
+ [-Tfactor ] :Optional :Consider T factor
+ [-T[ factor ]lim[it] Tlim (60 ).as(Real ) ] :Optional :The atom will be neglected
+ [-Centre ] :Optional :Filament-axis is x=0, y=0
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-C[ontour] contourLevel (0.0 ).as(Real ) ... ] :Variable :ContourLevel
+
+
+Usage of pdbRhoFit:
+ -ipdb : Filename of pdb file of atomic model
+ -imrc : Filename of mrc file of contour map
+ -omrc : Filename of mrc file of fitting results
+ -otxt : Filename of text file of fitting results
+ -opar : Filename of text file of fitting results
+ -opdb : Filename of pdb file with a max score after fitting results
+ -zmin : Initial value of z (should <= zmax)
+ -zmax : Final value of z
+ -zd : Delta z for fitting (should >0)
+ -phimin : Initial value of phi (should <= phimax; initial value of phi is 0)
+ -phimax : Final value of phi (should >0)
+ -phid : Delta phi for fitting (should >0)
+ -C : Contour level (variable and MUST be last option)
+ -Inverse: Protein has high density on the image
+ -Zminus : Atomic model shift to -z while fitting
+ -Tfactor: Consider temperature factor
+ -Tlim : The atoms whose T factor is above Tlim will be neglected
+ -Centre : Filament-axis is x=0, y=0
+ -c : Not used now
+ -m 0 : Count the atom number inside the contour.
+ 1 : Add the densities of atoms.
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbRhoFitTm: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbRhoFitTm</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbRhoFitTm</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbRhoFitTm
+Options:
+ [-i[nput]pdb[File] InPdb (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i[nput]mrc[File] InMrc (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput of ]mrc OutMrc (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-Sx Sx (50 ).as(Real ) ] :Essential :x of rotation axis
+ [-Sy Sy (110 ).as(Real ) ] :Essential :y of rotation axis
+ [-Sz Sz (110 ).as(Real ) ] :Essential :z of rotation axis
+ [-o[utput of ]txt OutTxt (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-o[utput of ]pdb OutPDB (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-xmin xmin (0 ).as(Real ) ] :Optional :xmin for fitting
+ [-xmax xmax (0 ).as(Real ) ] :Optional :xmax for fitting
+ [-xd[elta] xDelta (1 ).as(Real ) ] :Optional :delta x for fitting
+ [-ymin ymin (0 ).as(Real ) ] :Optional :ymin for fitting
+ [-ymax ymax (0 ).as(Real ) ] :Optional :ymax for fitting
+ [-yd[elta] yDelta (1 ).as(Real ) ] :Optional :delta y for fitting
+ [-zmin zmin (0 ).as(Real ) ] :Optional :zmin for fitting
+ [-zmax zmax (82 ).as(Real ) ] :Optional :zmax for fitting
+ [-zd[elta] zDelta (1 ).as(Real ) ] :Optional :delta z for fitting
+ [-E[uler]A[ngle] EulerAngle (ZOYS ).as(String ) ] :Optional :Euler Angle for three-angle
+ [-phimin phimin (0 ).as(Real ) ] :Optional :phimin for fitting(degree)
+ [-phimax phimax (194 ).as(Real ) ] :Optional :phimax for fitting(degree)
+ [-phid[elta] phiDelta (2 ).as(Real ) ] :Optional :delta phi for fitting(degree)
+ [-psimin psimin (0 ).as(Real ) ] :Optional :psimin for fitting(degree)
+ [-psimax psimax (0 ).as(Real ) ] :Optional :psimax for fitting(degree)
+ [-psid[elta] psiDelta (2 ).as(Real ) ] :Optional :delta psi for fitting(degree)
+ [-thetamin thetamin (0 ).as(Real ) ] :Optional :thetamin for fitting(degree)
+ [-thetamax thetamax (0 ).as(Real ) ] :Optional :thetamax for fitting(degree)
+ [-thetad[elta] thetaDelta (2 ).as(Real ) ] :Optional :delta theta for fitting(degree)
+ [-n[ormalize]w[eight]normalizeWeight (100000000.0).as(Real ) ] :Optional :weight for normalize
+ [-n[ormalize]C[ontour]normalizeContour (0.0 ).as(Real ) ] :Optional :Contour Level for Normalize
+ [-I[nverse] ] :Optional :Black is High Density.
+ [-Zminus ] :Optional :Shift to -z
+ [-Tfactor ] :Optional :Consider T factor
+ [-T[ factor ]lim[it] Tlim (60 ).as(Real ) ] :Optional :The atom will be neglected
+ [-Centre ] :Optional :Filament-axis is x=0, y=0
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-C[ontour] contourLevel (0.0 ).as(Real ) ... ] :Variable :ContourLevel
+
+
+Usage of pdbRhoFitTm:
+ -ipdb : Filename of pdb file of atomic model
+ -imrc : Filename of mrc file of contour map
+ -omrc : Filename of mrc file of fitting results
+ -otxt : Filename of text file of fitting results
+ -opdb : Filename of pdb file with a max score after fitting results
+ -zmin : Initial value of z (should <= zmax)
+ -zmax : Final value of z
+ -zd : Delta z for fitting (should >0)
+ -phimin : Initial value of phi (should <= phimax; initial value of phi is 0)
+ -phimax : Final value of phi (should >0)
+ -phid : Delta phi for fitting (should >0)
+ -C : Contour level (variable and MUST be last option)
+ -Inverse: Protein has high density on the image
+ -Sx : x of rotation axis
+ -Sy : y of rotation axis
+ -Sz : z of rotation axis
+ -Zminus : Atomic model shift to -z while fitting
+ -Tfactor: Consider temperature factor
+ -Tlim : The atoms whose T factor is above Tlim will be neglected
+ -Centre : Filament-axis is x=0, y=0
+ -c : Not used now
+ -m 0 : Count the atom number inside the contour.
+ 1 : Add the densities of atoms.
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbTwoProteinFit: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbTwoProteinFit</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbTwoProteinFit</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbTwoProteinFit
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i[nput]res[idue] InResidue (NULL ).as(inFile ) ] :Optional :ResidueInformationOfInputData
+ [-i[nput]sel[ectResidue]SelectIn (NULL ).as(outFile ) ] :Optional :Output: Selected residue of in after fitting
+ [-r[ef] Ref (NULL ).as(inFile ) ] :Essential :ReferenceDataFile
+ [-r[ef]res[idue] RefResidue (NULL ).as(inFile ) ] :Optional :ResidueInfomationOfReferenceData
+ [-r[ef]sel[ectResidue]SelectRef (NULL ).as(outFile ) ] :Optional :Output: Selected residue of after fitting
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-o[utput]Matrix Matrix (stdout ).as(outFile ) ] :Optional :OutputMatrix
+ [-o[utput]Param Param (stdout ).as(outFile ) ] :Optional :OutputParam
+ [-o[utput]Dis[tance] outDis (stdout ).as(outFile ) ] :Optional :Output: PDB Distance as Temp
+ [-o[utput]Dis[tance]2outDis2 (stdout ).as(outFile ) ] :Optional :Output: Distance List for Ca
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+>>>> Input and Reference File Format<<<<
+ResidueNumberToBeFitted
+...
+If |, all residules are sellected till the residue in the next line
+</PRE>
+</BODY>
+</HTML>
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