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base: Commit

This repository is a base of Eos.


Commit MetaInfo

Revision789628b1e9341b2d0bea8e08874fed573b4c5b5e (tree)
Time2015-06-08 05:55:07
AuthorTakuo Yasunaga <yasunaga@bio....>
CommiterTakuo Yasunaga

Log Message

Bug fixed and rebuild:
lmrcImageCopy

Change Summary

Incremental Difference

--- a/.Source
+++ /dev/null
@@ -1,22 +0,0 @@
1-SOURCE=\
2-Integration \
3-PrevReleased \
4-backup \
5-bin \
6-data \
7-database \
8-distribute \
9-env \
10-hostdepend \
11-include \
12-lib \
13-optional \
14-others \
15-others2 \
16-pione \
17-sbin \
18-src \
19-tutorial \
20-util \
21-zephyr \
22-#LastSource
--- a/.Source.org
+++ /dev/null
@@ -1,22 +0,0 @@
1-SOURCE=\
2-Integration \
3-PrevReleased \
4-backup \
5-bin \
6-data \
7-database \
8-distribute \
9-env \
10-hostdepend \
11-include \
12-lib \
13-optional \
14-others \
15-others2 \
16-pione \
17-sbin \
18-src \
19-tutorial \
20-util \
21-zephyr \
22-#LastSource
--- /dev/null
+++ b/bin/mrcImage3DPeakGet
@@ -0,0 +1 @@
1+../sbin/MachineIndependent
\ No newline at end of file
--- /dev/null
+++ b/bin/mrcImageSNEstimate
@@ -0,0 +1 @@
1+../sbin/MachineIndependent
\ No newline at end of file
--- a/bin/wish/Display2/tclIndex
+++ b/bin/wish/Display2/tclIndex
@@ -49,7 +49,6 @@ set auto_index(menuMultiRoiOKCommand) [list source [file join $dir Display2MenuR
4949 set auto_index(menuMultiRoiAllDeleteCommand) [list source [file join $dir Display2MenuROI.wish]]
5050 set auto_index(menuMultiRoiDeleteCommand) [list source [file join $dir Display2MenuROI.wish]]
5151 set auto_index(menuEditCreate) [list source [file join $dir Display2MenuROI.wish]]
52-set auto_index(fft2dCmd) [list source [file join $dir fft2dCmd.wish]]
5352 set auto_index(layerLineRecreate) [list source [file join $dir LayerLineUtil.wish]]
5453 set auto_index(layerLineCreate) [list source [file join $dir LayerLineUtil.wish]]
5554 set auto_index(layerLineClear) [list source [file join $dir LayerLineUtil.wish]]
@@ -132,3 +131,4 @@ set auto_index(sectionClearAll) [list source [file join $dir SectionUtil.wish]]
132131 set auto_index(sectionClear) [list source [file join $dir SectionUtil.wish]]
133132 set auto_index(sectionChange) [list source [file join $dir SectionUtil.wish]]
134133 set auto_index(unitCellRecreate) [list source [file join $dir UnitCell.wish]]
134+set auto_index(fft2dCmd) [list source [file join $dir fft2dCmd.wish]]
--- a/include/dmFile.h
+++ b/include/dmFile.h
@@ -135,6 +135,7 @@ typedef struct dmFile3Tag {
135135 char seperator[4];
136136 dmFileInteger4 ninfo;
137137 dmFileInteger4* info;
138+ long pValue; // Offset
138139 void* value; // Array or value
139140 void** value2; // Struct
140141 void** value3; // Array of Struct
@@ -151,6 +152,7 @@ typedef struct dmFile4Tag {
151152 char seperator[4];
152153 dmFileInteger8 ninfo;
153154 dmFileInteger8* info;
155+ long pValue;
154156 void* value; // Array or value
155157 void** value2; // Struct
156158 void** value3; // Array of Struct
--- /dev/null
+++ b/include/eosBayes.h
@@ -0,0 +1,23 @@
1+#ifndef EOS_BAYES_H
2+#define EOS_BAYES_H
3+
4+typedef struct eosBayesDistribution {
5+ float min;
6+ float max;
7+ float delta;
8+ int n;
9+ float* prob;
10+} eosBayesDistribution;
11+
12+
13+typedef struct eosBayes {
14+ int numDistribution;
15+ eosBayesDistribution* prior;
16+ eosBayesDistribution* posterior;
17+
18+ int numLikelihood;
19+ eosBayesDistribution* likelihood;
20+} eosBayes;
21+
22+
23+#endif /* EOS_BAYES_H */
--- a/include/lmrcImageRadialDistribution.h
+++ b/include/lmrcImageRadialDistribution.h
@@ -20,6 +20,9 @@ typedef struct lmrcImageRadialDistributionInfo {
2020 float Cx;
2121 float Cy;
2222 int flagAverage;
23+ int flagAzimuth;
24+ int NAzimuth;
25+ floatVector* azimuth;
2326 } lmrcImageRadialDistributionInfo;
2427 /* struct end */
2528
--- a/src/Objects/DataManip/dmFile/doc/dmFile.html
+++ b/src/Objects/DataManip/dmFile/doc/dmFile.html
@@ -146,6 +146,7 @@ typedef struct dmFile3Tag {
146146 char seperator[4];
147147 dmFileInteger4 ninfo;
148148 dmFileInteger4* info;
149+ long pValue; // Offset
149150 void* value; // Array or value
150151 void** value2; // Struct
151152 void** value3; // Array of Struct
@@ -162,6 +163,7 @@ typedef struct dmFile4Tag {
162163 char seperator[4];
163164 dmFileInteger8 ninfo;
164165 dmFileInteger8* info;
166+ long pValue;
165167 void* value; // Array or value
166168 void** value2; // Struct
167169 void** value3; // Array of Struct
--- a/src/Objects/DataManip/mrcImage/src/mrcImageCopy.c
+++ b/src/Objects/DataManip/mrcImage/src/mrcImageCopy.c
@@ -12,6 +12,8 @@
1212 static char __sccs_id[] = "@(#)mrcImageCopy ver1.1; Date:96/05/08 @(#)";
1313 #include <math.h>
1414 #include <stdlib.h>
15+#define DEBUG
16+#include "genUtil.h"
1517 #include "../inc/mrcImage.h"
1618
1719 void
@@ -22,14 +24,17 @@ lmrcImageCopy(mrcImage* dst, mrcImage* src, mrcImageParaTypeRealCoord to)
2224 mrcImageParaTypeInteger x, y, z;
2325 int k;
2426
25- for(iz=0; iz<dst->HeaderN.z; iz++) {
26- for(iy=0; iy<dst->HeaderN.y; iy++) {
27- for(ix=0; ix<dst->HeaderN.x; ix++) {
28- x = (int)(ix - to.x + 0.5);
29- y = (int)(iy - to.y + 0.5);
30- z = (int)(iz - to.z + 0.5);
31- mrcPixelDataGet(src, x, y, z, &data, mrcPixelRePart, mrcPixelHowNearest);
32- mrcPixelDataSet(dst, ix, iy, iz, data, mrcPixelRePart);
27+ DEBUGPRINT3("to: %g %g %g in lmrcImageCopy\n", to.x, to.y, to.z);
28+ DEBUGPRINT3("src: %d %d %d in lmrcImageCopy\n", src->HeaderN.x, src->HeaderN.y, src->HeaderN.z);
29+ DEBUGPRINT3("dst: %d %d %d in lmrcImageCopy\n", dst->HeaderN.x, dst->HeaderN.y, dst->HeaderN.z);
30+ for(iz=0; iz<src->HeaderN.z; iz++) {
31+ for(iy=0; iy<src->HeaderN.y; iy++) {
32+ for(ix=0; ix<src->HeaderN.x; ix++) {
33+ x = (int)(ix + to.x + 0.5);
34+ y = (int)(iy + to.y + 0.5);
35+ z = (int)(iz + to.z + 0.5);
36+ mrcPixelDataGet(src, ix, iy, iz, &data, mrcPixelRePart, mrcPixelHowNearest);
37+ mrcPixelDataSet(dst, x, y, z, data, mrcPixelRePart);
3338 }
3439 }
3540 }
--- a/src/Objects/DataManip/pdbFile/src/pdbUtil.c
+++ b/src/Objects/DataManip/pdbFile/src/pdbUtil.c
@@ -610,29 +610,57 @@ pdbRecordIsNearby(pdbRecord record1,pdbRecord record2)
610610 pdbFileParaTypeInteger
611611 pdbZValueGet(pdbFile* pdb)
612612 {
613- if( pdb->PDB->AtomName[1] == 'H') {
614- return 1;
615- } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'C') {
616- return 6;
617- } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'N') {
618- return 7;
619- } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'O') {
620- return 8;
621- } else if(pdb->PDB->AtomName[0] == 'M' && pdb->PDB->AtomName[1] == 'G') {
622- return 12;
623- } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'P') {
624- return 15;
625- } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'S') {
626- return 16;
613+ if( pdb->PDB->Footnote[6] == ' ' && pdb->PDB->Footnote[7] == 'H') {
614+ return 1;
615+ } else if(pdb->PDB->Footnote[6] == ' ' && pdb->PDB->Footnote[7] == 'C') {
616+ return 6;
617+ } else if(pdb->PDB->Footnote[6] == ' ' && pdb->PDB->Footnote[7] == 'N') {
618+ return 7;
619+ } else if(pdb->PDB->Footnote[6] == ' ' && pdb->PDB->Footnote[7] == 'O') {
620+ return 8;
621+ } else if(pdb->PDB->Footnote[6] == 'N' && pdb->PDB->Footnote[7] == 'A') {
622+ return 11;
623+ } else if(pdb->PDB->Footnote[6] == 'M' && pdb->PDB->Footnote[7] == 'G') {
624+ return 12;
625+ } else if(pdb->PDB->Footnote[6] == ' ' && pdb->PDB->Footnote[7] == 'P') {
626+ return 15;
627+ } else if(pdb->PDB->Footnote[6] == ' ' && pdb->PDB->Footnote[7] == 'S') {
628+ return 16;
629+ } else if(pdb->PDB->Footnote[6] == 'C' && pdb->PDB->Footnote[7] == 'L') {
630+ return 17;
631+ } else if(pdb->PDB->Footnote[6] == ' ' && pdb->PDB->Footnote[7] == 'K') {
632+ return 19;
633+ } else if(pdb->PDB->Footnote[6] == 'C' && pdb->PDB->Footnote[7] == 'A') {
634+ return 20;
635+ } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'H') {
636+ return 1;
637+ } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'C') {
638+ return 6;
639+ } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'N') {
640+ return 7;
641+ } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'O') {
642+ return 8;
643+ } else if(pdb->PDB->AtomName[0] == 'N' && pdb->PDB->AtomName[1] == 'A') {
644+ return 11;
645+ } else if(pdb->PDB->AtomName[0] == 'M' && pdb->PDB->AtomName[1] == 'G') {
646+ return 12;
647+ } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'P') {
648+ return 15;
649+ } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'S') {
650+ return 16;
627651 } else if(pdb->PDB->AtomName[0] == 'C' && pdb->PDB->AtomName[1] == 'L') {
628652 return 17;
629- } else if(pdb->PDB->AtomName[0] == 'C' && pdb->PDB->AtomName[1] == 'A') {
630- return 20;
653+ } else if(pdb->PDB->AtomName[0] == ' ' && pdb->PDB->AtomName[1] == 'K') {
654+ return 19;
655+ } else if(pdb->PDB->AtomName[0] == 'C' && pdb->PDB->AtomName[1] == 'A') {
656+ return 20;
631657 } else if(pdb->PDB->AtomName[0] == 'F' && pdb->PDB->AtomName[1] == 'E') {
632658 return 26;
633- } else {
634- fprintf(stderr, "Not supported element: %c%c to Carbon\n", pdb->PDB->AtomName[0], pdb->PDB->AtomName[1]);
635- return 6;
636- }
659+ } else {
660+ fprintf(stderr, "Not supported element: %c%c\n", pdb->PDB->Footnote[6], pdb->PDB->Footnote[7]);
661+ fprintf(stderr, "Not supported element: %c%c\n", pdb->PDB->AtomName[0], pdb->PDB->AtomName[1]);
662+ return 6;
663+ }
664+ return 6;
637665 }
638666
--- a/src/Objects/General/.Source
+++ b/src/Objects/General/.Source
@@ -17,6 +17,7 @@ SpecialNumber \
1717 String \
1818 Vector \
1919 dummy \
20+eosBayes \
2021 eosCuda \
2122 eosFunc \
2223 eosList \
--- a/src/Objects/General/.Source.org
+++ b/src/Objects/General/.Source.org
@@ -17,6 +17,7 @@ SpecialNumber \
1717 String \
1818 Vector \
1919 dummy \
20+eosBayes \
2021 eosCuda \
2122 eosFunc \
2223 eosList \
--- /dev/null
+++ b/src/Objects/General/eosBayes/.Source
@@ -0,0 +1,5 @@
1+SOURCE=\
2+doc \
3+inc \
4+src \
5+#LastSource
--- /dev/null
+++ b/src/Objects/General/eosBayes/.Source.org
@@ -0,0 +1,5 @@
1+SOURCE=\
2+doc \
3+inc \
4+src \
5+#LastSource
--- a/src/Objects/General/eosBayes/src/.CCHeader
+++ b/src/Objects/General/eosBayes/src/.CCHeader
@@ -0,0 +1,2 @@
1+CCHeader = \
2+
--- a/src/Objects/General/eosBayes/src/.CHeader
+++ b/src/Objects/General/eosBayes/src/.CHeader
@@ -0,0 +1,2 @@
1+CHeader = \
2+
--- a/src/Objects/General/eosBayes/src/.Ruby
+++ b/src/Objects/General/eosBayes/src/.Ruby
@@ -0,0 +1,2 @@
1+Ruby = \
2+
--- a/src/Objects/General/eosBayes/src/.Wish
+++ b/src/Objects/General/eosBayes/src/.Wish
@@ -0,0 +1,2 @@
1+Wish = \
2+
--- a/src/Tools/.Source
+++ b/src/Tools/.Source
@@ -2,6 +2,7 @@ SOURCE=\
22 Cluster \
33 Coord \
44 DCDFile \
5+DataManip \
56 Integration \
67 admin \
78 array \
--- a/src/Tools/.Source.org
+++ b/src/Tools/.Source.org
@@ -2,7 +2,6 @@ SOURCE=\
22 Cluster \
33 Coord \
44 DCDFile \
5-DataManip \
65 Integration \
76 admin \
87 array \
--- a/src/Tools/Cluster/.Source
+++ /dev/null
@@ -1,5 +0,0 @@
1-SOURCE=\
2-clusterLog2ToLog \
3-clusterLogASCII2Binary \
4-clusterShow \
5-#LastSource
--- a/src/Tools/Coord/.Source
+++ /dev/null
@@ -1,4 +0,0 @@
1-SOURCE=\
2-coordRotation \
3-pointsSetToPDB \
4-#LastSource
--- a/src/Tools/DCDFile/.Source
+++ /dev/null
@@ -1,11 +0,0 @@
1-SOURCE=\
2-dcdAtomChangeDistanceFromAtom \
3-dcdAtomDistanceDistribution \
4-dcdCompareCA \
5-dcdDistanceAtomBetweenAtom \
6-dcdFilePrint \
7-dcdInfo \
8-dcdSelectAtoms \
9-dcdSerectAtom \
10-dcdTimeSeriesBehavior \
11-#LastSource
--- /dev/null
+++ b/src/Tools/DataManip/.Source.org
@@ -0,0 +1,4 @@
1+SOURCE=\
2+bmp2mrc \
3+dm \
4+#LastSource
--- /dev/null
+++ b/src/Tools/DataManip/Makefile
@@ -0,0 +1,119 @@
1+include ../../Config/Define.inc
2+include ../Config/Define.inc
3+include Config/Define.inc
4+include .Source
5+
6+all:
7+ for dir in ${SOURCE} ; \
8+ do \
9+ if [ -d $${dir} ] ; then \
10+ $(CD) $${dir}; make all; $(CD) ..; \
11+ fi \
12+ done
13+
14+install:
15+ for dir in ${SOURCE} ; \
16+ do \
17+ if [ -d $${dir} ] ; then \
18+ $(CD) $${dir}; make install; $(CD) ..; \
19+ fi \
20+ done
21+
22+put:
23+ for dir in ${SOURCE} ; \
24+ do \
25+ if [ -d $${dir} ] ; then \
26+ $(CD) $${dir}; make put; $(CD) ..; \
27+ fi \
28+ done
29+
30+putSF:
31+ if [ -f private ] ; then \
32+ echo "$(WORLDNAME)/$(CLASSNAME) is private " ; \
33+ else \
34+ for dir in ${SOURCE} ; \
35+ do \
36+ if [ -d $${dir} ] ; then \
37+ $(CD) $${dir}; make putSF; $(CD) ..; \
38+ fi \
39+ done \
40+ fi
41+
42+clean:
43+ for dir in ${SOURCE} ; \
44+ do \
45+ $(CD) $${dir}; make clean; $(CD) ..; \
46+ done
47+
48+check:
49+ @for dir in ${SOURCE} ; do \
50+ if [ -d $${dir} ] ; then \
51+ $(CD) $${dir}; \
52+ echo $${dir}; \
53+ $(RM) Makefile; \
54+ $(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/Makefile Makefile ; \
55+ make check; \
56+ $(CD) ..; \
57+ fi \
58+ done
59+
60+update:
61+ @for dir in ${SOURCE} ; do \
62+ if [ -d $${dir} ] ; then \
63+ $(CD) $${dir}; \
64+ echo $${dir}; \
65+ $(RM) Makefile; \
66+ $(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/Makefile Makefile ; \
67+ make update; \
68+ $(CD) ..; \
69+ fi \
70+ done
71+
72+depend: check
73+ @for dir in ${SOURCE} ; \
74+ do \
75+ $(CD) $${dir}; make depend; $(CD) ..; \
76+ done
77+
78+backup:
79+ cd ../../..; \
80+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
81+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
82+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
83+ tar uvf ${EOS_HOME}/backup/EosBase.tar .[A-z]*
84+ @for dir in ${SOURCE} ; \
85+ do \
86+ $(CD) $${dir}; make backup; $(CD) ..; \
87+ done
88+
89+backup-all:
90+ cd ../../..; \
91+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
92+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
93+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
94+ tar rvf ${EOS_HOME}/backup/EosBase.tar .[A-z]*
95+ @for dir in ${SOURCE} ; \
96+ do \
97+ $(CD) $${dir}; make backup; $(CD) ..; \
98+ done
99+
100+distribute:
101+ cd ../../..; \
102+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
103+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
104+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
105+ @for dir in ${SOURCE} ; \
106+ do \
107+ $(CD) $${dir}; make distribute; $(CD) ..; \
108+ done
109+
110+distribute-all:
111+ cd ../../..; \
112+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
113+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
114+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
115+ @for dir in ${SOURCE} ; \
116+ do \
117+ $(CD) $${dir}; make distribute-all; $(CD) ..; \
118+ done
119+
--- a/src/Tools/Makefile
+++ /dev/null
@@ -1 +0,0 @@
1-/Users/tacyas/Eos/src/Config/Template/ToolsHomeTemplate.Dir/Makefile
\ No newline at end of file
--- /dev/null
+++ b/src/Tools/Makefile
@@ -0,0 +1,5 @@
1+include ../Config/Define.inc
2+include Config/Define.inc
3+include .Source
4+
5+include Config/Target.inc
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImage3DPeakGet/src/mrcImage3DPeakGet.html
@@ -0,0 +1,19 @@
1+<HTML>
2+<HEAD>
3+<TITLE>mrcImage3DPeakGet</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>mrcImage3DPeakGet</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: mrcImage3DPeakGet
10+Options:
11+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:3D
12+ [-I[nformation] Info (stdin ).as(inFile::ASCII ) ] :Optional :Input:ROI Info
13+ [-o[utput] Out (stdout ).as(outFile::ASCII ) ] :Optional :Output:Positon
14+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
15+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
16+----- Additional Usage -----
17+</PRE>
18+</BODY>
19+</HTML>
--- a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/mrcImageAutoCorrelationWithWindowing.html
+++ b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/mrcImageAutoCorrelationWithWindowing.html
@@ -8,9 +8,10 @@
88 <PRE>
99 Usage: mrcImageAutoCorrelationWithWindowing
1010 Options:
11- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
12- [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
13- [-O[utput] OutWin (NULL ).as(outFile ) ] :Optional :Output WindowedFile
11+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input
12+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output
13+ [-o[utput]c[entre] OutCentre (NULL ).as(outFile::mrcImage ) ] :Optional :OutputDataFile
14+ [-O[utput] OutWin (NULL ).as(outFile::mrcImage ) ] :Optional :Output WindowedFile
1415 [-W[indowing]y Wy (6 ).as(Real ) ] :Optional :Window Height: N.y * 1/Wy
1516 [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
1617 [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
--- a/src/Tools/mrcImage/mrcImageDensityInfo/src/mrcImageDensityInfo.html
+++ b/src/Tools/mrcImage/mrcImageDensityInfo/src/mrcImageDensityInfo.html
@@ -10,7 +10,7 @@ Usage: mrcImageDensityInfo
1010 Options:
1111 [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
1212 [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
13- [-C[ontour] Contour (10 ).as(Real ) ] :Optional :ContourLevel: 10 6.950489e-310ach
13+ [-C[ontour] Contour (10 ).as(Real ) ] :Optional :ContourLevel: 10 5.533535e-322ach
1414 [-log Log (NULL ).as(appendFile ) ] :Optional :OutputDataFile
1515 [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
1616 [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageSNEstimate/src/mrcImageSNEstimate.html
@@ -0,0 +1 @@
1+/bin/bash: mrcImageSNEstimate: No such file or directory
--- a/src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.c
+++ b/src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.c
@@ -150,6 +150,15 @@ main(int argc, char* argv[])
150150 (info.mode&HowToCreateImageBit));
151151 for(iy=0; iy < info.rotny; iy+= droty) {
152152 DEBUGPRINT2("%g %g\n", ix, iy);
153+
154+#ifdef DEBUG
155+ {
156+ pdbFileTop(&pdb);
157+ pdbFileNextAtom(&pdb);
158+ DEBUGPRINT3("(x, y, z)=(%g, %g %g)\n", pdb.PDB->Coord.x, pdb.PDB->Coord.y, pdb.PDB->Coord.z);
159+ }
160+#endif
161+
153162 if(!info.flagRotMode) {
154163 roty = ((double)iy)/info.rotny*2.0*M_PI;
155164 pdbRotationZXY(&pdb, rotx, -roty, -rotz);
@@ -158,8 +167,26 @@ main(int argc, char* argv[])
158167 pdbRotationFollowingEulerAngle(&pdb, info.RotMode, -roty, rotx, -rotz);
159168 }
160169
170+#ifdef DEBUG
171+ {
172+ pdbFileTop(&pdb);
173+ pdbFileNextAtom(&pdb);
174+ DEBUGPRINT3("(x, y, z)=(%g, %g %g)\n", pdb.PDB->Coord.x, pdb.PDB->Coord.y, pdb.PDB->Coord.z);
175+ }
176+#endif
177+
161178 DEBUGPRINT3("rot: (%g %g %g) \n", rotx*DEGREE, roty*DEGREE, rotz*DEGREE);
179+
162180 lpdb2mrc2d(&mrc, &pdb, &linfo, 'z', 0);
181+#ifdef DEBUG
182+ {
183+ char s[1024];
184+
185+ sprintf(s, "/tmp/test.mrc.%03d", (int)zsection);
186+
187+ mrcFileWrite(&mrc, s, "tmp", 0);
188+ }
189+#endif
163190
164191 if(!info.flagRotMode) {
165192 pdbRotationYXZ(&pdb, -rotx, roty, rotz);
@@ -174,7 +201,15 @@ main(int argc, char* argv[])
174201 to.y = fmod(to.y*info.ny, out.HeaderN.y);
175202 DEBUGPRINT2("map %f %f\n", to.x, to.y);
176203 to.z = 0.0;
204+ DEBUGPRINT3("to: %f %f %f\n", to.x, to.y, to.z);
177205 lmrcImageCopy(&out, &mrc, to);
206+#ifdef DEBUG
207+ {
208+ char s[1024];
209+ sprintf(s, "/tmp/test.2d.%03d", (int)zsection);
210+ mrcFileWrite(&out, s, "tmp", 0);
211+ }
212+#endif
178213 }
179214 if(info.flagOut3D) {
180215 to.x = 0.0;
@@ -188,6 +223,7 @@ main(int argc, char* argv[])
188223 out3D.Tailer[(int)zsection].Cont.Rot1 = -roty;
189224 out3D.Tailer[(int)zsection].Cont.Rot2 = rotx;
190225 out3D.Tailer[(int)zsection].Cont.Rot3 = -rotz;
226+ DEBUGPRINT3("to: %f %f %f\n", to.x, to.y, to.z);
191227 lmrcImageCopy(&out3D, &mrc, to);
192228 zsection += 1.0;
193229 }
--- a/src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.html
+++ b/src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.html
@@ -36,6 +36,7 @@ Options:
3636 [-w[eight] Weight (1.0 ).as(Real ) ] :Optional :weight
3737 [-sig[ma] Sigma (0.0 ).as(Real ) ] :Optional :Sigma[A]:Atom radius
3838 [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
39+ [-cuda cudaDeviceID (0 ).as(Integer ) ] :Optional :UseCuda
3940 [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode: 0 Merc; 1: Earth
4041 ----- Attention1 -----
4142 If both of -s and -startEA, first -s and second -startEA will be performed
--- a/src/Tools/pdbUtil/pdb2mrc2d/src/test/Makefile
+++ b/src/Tools/pdbUtil/pdb2mrc2d/src/test/Makefile
@@ -16,7 +16,12 @@ exec:
1616
1717 exec2:
1818 @echo "----- Execution Check -----"
19- ../$(OSTYPE)/$(OBJECTNAME) -i data/121p.shift.pdb -o data/121p.mrc2d2 -O data/121p.mrc2dStack2 -s -32 -32 -n 32 32 -d 2 2 -Rot 12 12 -m 1 -sig 3
19+ ../$(OSTYPE)/$(OBJECTNAME) -i data/121p.shift.pdb -o data/121p.mrc2d2 -O data/121p.mrc2dStack2 -s -32 -32 -n 32 32 -d 2 2 -Rot 12 12 -m 3 -sig 3
20+ @echo "----- Calc check -----"
21+
22+exec3:
23+ @echo "----- Execution Check -----"
24+ ../$(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
2025 @echo "----- Calc check -----"
2126
2227 clean:
--- a/src/Tools/pdbUtil/pdb2mrc2dWithCTF/src/pdb2mrc2dWithCTF.c
+++ b/src/Tools/pdbUtil/pdb2mrc2dWithCTF/src/pdb2mrc2dWithCTF.c
@@ -89,6 +89,7 @@ additionalUsage()
8989 * * pdbZValueGet
9090 * * return value: Atomic Mass of the current atom
9191 */
92+/*
9293 int
9394 pdbZValueGet(pdbRecord* current)
9495 {
@@ -139,7 +140,7 @@ pdbZValueGet(pdbRecord* current)
139140 }
140141 return 1;
141142 }
142-
143+*/
143144 void
144145 lpdb2mrc2dWithCTF(mrcImage* out, pdbFile* pdb, lpdb2mrc2dWithCTFInfo* linfo, ctfInfo* ctf, int mode)
145146 {
@@ -189,7 +190,7 @@ lpdb2mrc2dWithCTF(mrcImage* out, pdbFile* pdb, lpdb2mrc2dWithCTFInfo* linfo, ctf
189190 if(i%100==0) {
190191 fprintf(stderr, "%d\n", i);
191192 }
192- Z = pdbZValueGet(pdb->PDB);
193+ Z = pdbZValueGet(pdb);
193194 R = aH *pow(Z, -1.0/3.0);
194195
195196 mrcInit(&sub, NULL);
@@ -241,4 +242,3 @@ lpdb2mrc2dWithCTF(mrcImage* out, pdbFile* pdb, lpdb2mrc2dWithCTFInfo* linfo, ctf
241242 }
242243 }
243244 }
244-
--- a/src/Tools/pdbUtil/pdb2mrc2dWithCTF/src/pdb2mrc2dWithCTF.html
+++ b/src/Tools/pdbUtil/pdb2mrc2dWithCTF/src/pdb2mrc2dWithCTF.html
@@ -1 +1,37 @@
1-/bin/bash: pdb2mrc2dWithCTF: No such file or directory
1+<HTML>
2+<HEAD>
3+<TITLE>pdb2mrc2dWithCTF</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>pdb2mrc2dWithCTF</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: pdb2mrc2dWithCTF
10+Options:
11+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: PDB
12+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: MRC
13+ [-N Nx (2048 ).as(Integer )
14+ Ny (2048 ).as(Integer ) ] :Optional :Input: Nx Ny [pixel]
15+ [-d dx (1.72 ).as(Real )
16+ dy (1.72 ).as(Real ) ] :Optional :Input: dx dy [A]
17+ [-Centre cx (0 ).as(Real )
18+ cy (0 ).as(Real )
19+ cz (0 ).as(Real ) ] :Optional :Input: CentreX CentreY [A]
20+ [-n nx (64 ).as(Integer )
21+ ny (64 ).as(Integer ) ] :Optional :Input: nx ny for subimage [pixel]
22+ [-kV kV (200. ).as(Real ) ] :Optional :kV
23+ [-Cs Cs (1.7 ).as(Real ) ] :Optional :Cs
24+ [-d[e]f[ocus] Defocus (10000 ).as(Real ) ] :Optional :Defocus [A] at z = 0
25+ [-A[overP] AoverP (0.07 ).as(Real ) ] :Optional :AoverP
26+ [-Ain Ain (0.2 ).as(Real ) ] :Optional :Beta: IlluminationAngle [mrad]
27+ [-ctfMode ctfMode (33 ).as(Integer ) ] :Optional :ctfMode
28+ [-E[uler]A[ngle] EulerAngle (XEYS ).as(String )
29+ Rot1 (0 ).as(Real )
30+ Rot2 (0 ).as(Real )
31+ Rot3 (0 ).as(Real ) ] :Optional :EulerAngle: [degree]
32+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
33+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
34+----- Additional Usage -----
35+</PRE>
36+</BODY>
37+</HTML>
--- a/src/Tools/pdbUtil/pdb2mrc2dWithCTF/src/test/Makefile
+++ b/src/Tools/pdbUtil/pdb2mrc2dWithCTF/src/test/Makefile
@@ -11,7 +11,7 @@ help:
1111
1212 exec:
1313 @echo "----- Execution Check -----"
14- ../$(OSTYPE)/$(OBJECTNAME)
14+ ../$(OSTYPE)/$(OBJECTNAME) -i data/121p.pdb -o data/121p.mrc
1515 @echo "----- Calc check -----"
1616
1717 clean:
--- a/src/Tools/pdbUtil/pdbCrystalCreate/src/pdbCrystalCreate.html
+++ b/src/Tools/pdbUtil/pdbCrystalCreate/src/pdbCrystalCreate.html
@@ -1 +1,36 @@
1-/bin/bash: pdbCrystalCreate: No such file or directory
1+<HTML>
2+<HEAD>
3+<TITLE>pdbCrystalCreate</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>pdbCrystalCreate</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: pdbCrystalCreate
10+Options:
11+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input:PDB
12+ [-I[nfo] Info (NULL ).as(inFile ) ] :Essential :Input:Crystal Information
13+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output:PDB
14+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
15+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
16+----- Additional Usage -----
17+----- CrystalInfo -----
18+aAxis %15.6g %15.6g %15.6g
19+bAxis %15.6g %15.6g %15.6g
20+cAxis %15.6g %15.6g %15.6g
21+CellLength %15.6g %15.6g %15.6g
22+Origin %15.6g %15.6g %15.6g
23+N %15d %15d %15d
24+StartN %15d %15d %15d
25+SpaceGroup %15d
26+HelixInfo %10d %10d %10d
27+### Attention ###
28+Parameter Order is important: Dependent between CellLength and a|b|cAxis.
29+ Because each of aAxis, bAxis, cAxis must be a unit vector.
30+HelixInfo t u n
31+----- CrystalSpaceGroup -----
32+ 0 P1
33+ 1 HelicalSymmmetry
34+</PRE>
35+</BODY>
36+</HTML>
--- a/src/Tools/pdbUtil/pdbHelix/src/pdbHelix.html
+++ b/src/Tools/pdbUtil/pdbHelix/src/pdbHelix.html
@@ -1 +1,37 @@
1-/bin/bash: pdbHelix: No such file or directory
1+<HTML>
2+<HEAD>
3+<TITLE>pdbHelix</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>pdbHelix</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: pdbHelix
10+Options:
11+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
12+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
13+ [-3[D] Out3D (NULL ).as(outFile ) ] :Optional :OutputDataFile(3D-mrc)
14+ [-2[D] Out2D (NULL ).as(outFile ) ] :Optional :OutputDataFile(2D-mrc projection(y-z))
15+ [-d[elta] delta (5 ).as(Real ) ] :Optional :delta[A](mrc-file)
16+ [-p[delphi] delphi (165 ).as(Real ) ] :Essential :deltaPhi
17+ [-dp[delphi] deldelphi (5 ).as(Real ) ] :Optional :deltaDeltaPhi
18+ [-z[deltaz] delz (5 ).as(Real ) ] :Essential :deltaz
19+ [-n[Molecule] nMolecule (1 ).as(Integer ) ] :Essential :NumberOfMolecules
20+ [-nx nx (1 ).as(Integer ) ] :Optional :Pixel[Def:]
21+ [-ny ny (1 ).as(Integer ) ] :Optional :Pixel[Def:]
22+ [-nz nz (1 ).as(Integer ) ] :Optional :Pixel[Def:]
23+ [-Sx[tart] Startx (0.0 ).as(Real ) ] :Optional :Startx[A]
24+ [-Sy[tart] Starty (0.0 ).as(Real ) ] :Optional :Starty[A]
25+ [-Sz[tart] Startz (0.0 ).as(Real ) ] :Optional :Startz[A]
26+ [-w[eight] Weight (1.0 ).as(Real ) ] :Optional :Weight
27+ [-dx dx (2.5 ).as(Real ) ] :Optional :dx
28+ [-dy dy (2.5 ).as(Real ) ] :Optional :dy
29+ [-dz dz (2.5 ).as(Real ) ] :Optional :dz
30+ [-startn startn (0 ).as(Integer ) ] :Optional :start molecule's index
31+ [-startC startID (A ).as(Character ) ] :Optional :start chain ID
32+ [-deltaSeq deltaSeq (1000 ).as(Integer ) ] :Optional :start chain ID
33+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
34+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
35+</PRE>
36+</BODY>
37+</HTML>
--- a/src/Tools/pdbUtil/pdbMove/src/pdbMove.html
+++ b/src/Tools/pdbUtil/pdbMove/src/pdbMove.html
@@ -1 +1,28 @@
1-/bin/bash: pdbMove: No such file or directory
1+<HTML>
2+<HEAD>
3+<TITLE>pdbMove</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>pdbMove</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: pdbMove
10+Options:
11+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
12+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
13+ [-x X (0.0 ).as(Real ) ] :Optional :Move X[A]
14+ [-y Y (0.0 ).as(Real ) ] :Optional :Move Y[A]
15+ [-z Z (0.0 ).as(Real ) ] :Optional :Move Z[A]
16+ [-originTo toX (0.0 ).as(Real )
17+ toY (0.0 ).as(Real )
18+ toZ (0.0 ).as(Real ) ] :Optional :move (0,0,0) to (X,Y,Z)
19+ [-toOrigin fromX (0.0 ).as(Real )
20+ fromY (0.0 ).as(Real )
21+ fromZ (0.0 ).as(Real ) ] :Optional :move (X,Y,Z) to (0,0,0)
22+ [-GCtoOrigin ] :Optional :GC(Gravity Centre) to origin
23+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
24+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
25+----- Additional Usage -----
26+</PRE>
27+</BODY>
28+</HTML>
--- a/src/Tools/pdbUtil/pdbRhoFit/src/pdbRhoFit.html
+++ b/src/Tools/pdbUtil/pdbRhoFit/src/pdbRhoFit.html
@@ -1 +1,72 @@
1-/bin/bash: pdbRhoFit: No such file or directory
1+<HTML>
2+<HEAD>
3+<TITLE>pdbRhoFit</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>pdbRhoFit</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: pdbRhoFit
10+Options:
11+ [-i[nput]pdb[File] InPdb (NULL ).as(inFile ) ] :Essential :InputDataFile
12+ [-i[nput]mrc[File] InMrc (NULL ).as(inFile ) ] :Essential :InputDataFile
13+ [-o[utput of ]mrc OutMrc (NULL ).as(outFile ) ] :Essential :OutputDataFile
14+ [-o[utput of ]txt OutTxt (NULL ).as(outFile ) ] :Optional :OutputDataFile
15+ [-o[utput of ]par OutPar (stdout ).as(outFile ) ] :Optional :OutputDataFile
16+ [-o[utput of ]pdb OutPDB (NULL ).as(outFile ) ] :Optional :OutputDataFile
17+ [-xmin xmin (0 ).as(Real ) ] :Optional :xmin for fitting
18+ [-xmax xmax (0 ).as(Real ) ] :Optional :xmax for fitting
19+ [-xd[elta] xDelta (1 ).as(Real ) ] :Optional :delta x for fitting
20+ [-ymin ymin (0 ).as(Real ) ] :Optional :ymin for fitting
21+ [-ymax ymax (0 ).as(Real ) ] :Optional :ymax for fitting
22+ [-yd[elta] yDelta (1 ).as(Real ) ] :Optional :delta y for fitting
23+ [-zmin zmin (0 ).as(Real ) ] :Optional :zmin for fitting
24+ [-zmax zmax (82 ).as(Real ) ] :Optional :zmax for fitting
25+ [-zd[elta] zDelta (1 ).as(Real ) ] :Optional :delta z for fitting
26+ [-E[uler]A[ngle] EulerAngle (ZOYS ).as(String ) ] :Optional :Euler Angle for three-angle
27+ [-phimin phimin (0 ).as(Real ) ] :Optional :phimin for fitting(degree)
28+ [-phimax phimax (194 ).as(Real ) ] :Optional :phimax for fitting(degree)
29+ [-phid[elta] phiDelta (2 ).as(Real ) ] :Optional :delta phi for fitting(degree)
30+ [-psimin psimin (0 ).as(Real ) ] :Optional :psimin for fitting(degree)
31+ [-psimax psimax (0 ).as(Real ) ] :Optional :psimax for fitting(degree)
32+ [-psid[elta] psiDelta (2 ).as(Real ) ] :Optional :delta psi for fitting(degree)
33+ [-thetamin thetamin (0 ).as(Real ) ] :Optional :thetamin for fitting(degree)
34+ [-thetamax thetamax (0 ).as(Real ) ] :Optional :thetamax for fitting(degree)
35+ [-thetad[elta] thetaDelta (2 ).as(Real ) ] :Optional :delta theta for fitting(degree)
36+ [-n[ormalize]w[eight]normalizeWeight (100000000.0).as(Real ) ] :Optional :weight for normalize
37+ [-n[ormalize]C[ontour]normalizeContour (0.0 ).as(Real ) ] :Optional :Contour Level for Normalize
38+ [-I[nverse] ] :Optional :Black is High Density.
39+ [-Zminus ] :Optional :Shift to -z
40+ [-Tfactor ] :Optional :Consider T factor
41+ [-T[ factor ]lim[it] Tlim (60 ).as(Real ) ] :Optional :The atom will be neglected
42+ [-Centre ] :Optional :Filament-axis is x=0, y=0
43+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
44+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
45+ [-C[ontour] contourLevel (0.0 ).as(Real ) ... ] :Variable :ContourLevel
46+
47+
48+Usage of pdbRhoFit:
49+ -ipdb : Filename of pdb file of atomic model
50+ -imrc : Filename of mrc file of contour map
51+ -omrc : Filename of mrc file of fitting results
52+ -otxt : Filename of text file of fitting results
53+ -opar : Filename of text file of fitting results
54+ -opdb : Filename of pdb file with a max score after fitting results
55+ -zmin : Initial value of z (should <= zmax)
56+ -zmax : Final value of z
57+ -zd : Delta z for fitting (should >0)
58+ -phimin : Initial value of phi (should <= phimax; initial value of phi is 0)
59+ -phimax : Final value of phi (should >0)
60+ -phid : Delta phi for fitting (should >0)
61+ -C : Contour level (variable and MUST be last option)
62+ -Inverse: Protein has high density on the image
63+ -Zminus : Atomic model shift to -z while fitting
64+ -Tfactor: Consider temperature factor
65+ -Tlim : The atoms whose T factor is above Tlim will be neglected
66+ -Centre : Filament-axis is x=0, y=0
67+ -c : Not used now
68+ -m 0 : Count the atom number inside the contour.
69+ 1 : Add the densities of atoms.
70+</PRE>
71+</BODY>
72+</HTML>
--- a/src/Tools/pdbUtil/pdbRhoFitTm/src/pdbRhoFitTm.html
+++ b/src/Tools/pdbUtil/pdbRhoFitTm/src/pdbRhoFitTm.html
@@ -1 +1,76 @@
1-/bin/bash: pdbRhoFitTm: No such file or directory
1+<HTML>
2+<HEAD>
3+<TITLE>pdbRhoFitTm</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>pdbRhoFitTm</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: pdbRhoFitTm
10+Options:
11+ [-i[nput]pdb[File] InPdb (NULL ).as(inFile ) ] :Essential :InputDataFile
12+ [-i[nput]mrc[File] InMrc (NULL ).as(inFile ) ] :Essential :InputDataFile
13+ [-o[utput of ]mrc OutMrc (NULL ).as(outFile ) ] :Essential :OutputDataFile
14+ [-Sx Sx (50 ).as(Real ) ] :Essential :x of rotation axis
15+ [-Sy Sy (110 ).as(Real ) ] :Essential :y of rotation axis
16+ [-Sz Sz (110 ).as(Real ) ] :Essential :z of rotation axis
17+ [-o[utput of ]txt OutTxt (NULL ).as(outFile ) ] :Optional :OutputDataFile
18+ [-o[utput of ]pdb OutPDB (NULL ).as(outFile ) ] :Optional :OutputDataFile
19+ [-xmin xmin (0 ).as(Real ) ] :Optional :xmin for fitting
20+ [-xmax xmax (0 ).as(Real ) ] :Optional :xmax for fitting
21+ [-xd[elta] xDelta (1 ).as(Real ) ] :Optional :delta x for fitting
22+ [-ymin ymin (0 ).as(Real ) ] :Optional :ymin for fitting
23+ [-ymax ymax (0 ).as(Real ) ] :Optional :ymax for fitting
24+ [-yd[elta] yDelta (1 ).as(Real ) ] :Optional :delta y for fitting
25+ [-zmin zmin (0 ).as(Real ) ] :Optional :zmin for fitting
26+ [-zmax zmax (82 ).as(Real ) ] :Optional :zmax for fitting
27+ [-zd[elta] zDelta (1 ).as(Real ) ] :Optional :delta z for fitting
28+ [-E[uler]A[ngle] EulerAngle (ZOYS ).as(String ) ] :Optional :Euler Angle for three-angle
29+ [-phimin phimin (0 ).as(Real ) ] :Optional :phimin for fitting(degree)
30+ [-phimax phimax (194 ).as(Real ) ] :Optional :phimax for fitting(degree)
31+ [-phid[elta] phiDelta (2 ).as(Real ) ] :Optional :delta phi for fitting(degree)
32+ [-psimin psimin (0 ).as(Real ) ] :Optional :psimin for fitting(degree)
33+ [-psimax psimax (0 ).as(Real ) ] :Optional :psimax for fitting(degree)
34+ [-psid[elta] psiDelta (2 ).as(Real ) ] :Optional :delta psi for fitting(degree)
35+ [-thetamin thetamin (0 ).as(Real ) ] :Optional :thetamin for fitting(degree)
36+ [-thetamax thetamax (0 ).as(Real ) ] :Optional :thetamax for fitting(degree)
37+ [-thetad[elta] thetaDelta (2 ).as(Real ) ] :Optional :delta theta for fitting(degree)
38+ [-n[ormalize]w[eight]normalizeWeight (100000000.0).as(Real ) ] :Optional :weight for normalize
39+ [-n[ormalize]C[ontour]normalizeContour (0.0 ).as(Real ) ] :Optional :Contour Level for Normalize
40+ [-I[nverse] ] :Optional :Black is High Density.
41+ [-Zminus ] :Optional :Shift to -z
42+ [-Tfactor ] :Optional :Consider T factor
43+ [-T[ factor ]lim[it] Tlim (60 ).as(Real ) ] :Optional :The atom will be neglected
44+ [-Centre ] :Optional :Filament-axis is x=0, y=0
45+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
46+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
47+ [-C[ontour] contourLevel (0.0 ).as(Real ) ... ] :Variable :ContourLevel
48+
49+
50+Usage of pdbRhoFitTm:
51+ -ipdb : Filename of pdb file of atomic model
52+ -imrc : Filename of mrc file of contour map
53+ -omrc : Filename of mrc file of fitting results
54+ -otxt : Filename of text file of fitting results
55+ -opdb : Filename of pdb file with a max score after fitting results
56+ -zmin : Initial value of z (should <= zmax)
57+ -zmax : Final value of z
58+ -zd : Delta z for fitting (should >0)
59+ -phimin : Initial value of phi (should <= phimax; initial value of phi is 0)
60+ -phimax : Final value of phi (should >0)
61+ -phid : Delta phi for fitting (should >0)
62+ -C : Contour level (variable and MUST be last option)
63+ -Inverse: Protein has high density on the image
64+ -Sx : x of rotation axis
65+ -Sy : y of rotation axis
66+ -Sz : z of rotation axis
67+ -Zminus : Atomic model shift to -z while fitting
68+ -Tfactor: Consider temperature factor
69+ -Tlim : The atoms whose T factor is above Tlim will be neglected
70+ -Centre : Filament-axis is x=0, y=0
71+ -c : Not used now
72+ -m 0 : Count the atom number inside the contour.
73+ 1 : Add the densities of atoms.
74+</PRE>
75+</BODY>
76+</HTML>
--- a/src/Tools/pdbUtil/pdbTwoProteinFit/src/pdbTwoProteinFit.html
+++ b/src/Tools/pdbUtil/pdbTwoProteinFit/src/pdbTwoProteinFit.html
@@ -1 +1,30 @@
1-/bin/bash: pdbTwoProteinFit: No such file or directory
1+<HTML>
2+<HEAD>
3+<TITLE>pdbTwoProteinFit</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>pdbTwoProteinFit</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: pdbTwoProteinFit
10+Options:
11+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
12+ [-i[nput]res[idue] InResidue (NULL ).as(inFile ) ] :Optional :ResidueInformationOfInputData
13+ [-i[nput]sel[ectResidue]SelectIn (NULL ).as(outFile ) ] :Optional :Output: Selected residue of in after fitting
14+ [-r[ef] Ref (NULL ).as(inFile ) ] :Essential :ReferenceDataFile
15+ [-r[ef]res[idue] RefResidue (NULL ).as(inFile ) ] :Optional :ResidueInfomationOfReferenceData
16+ [-r[ef]sel[ectResidue]SelectRef (NULL ).as(outFile ) ] :Optional :Output: Selected residue of after fitting
17+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
18+ [-o[utput]Matrix Matrix (stdout ).as(outFile ) ] :Optional :OutputMatrix
19+ [-o[utput]Param Param (stdout ).as(outFile ) ] :Optional :OutputParam
20+ [-o[utput]Dis[tance] outDis (stdout ).as(outFile ) ] :Optional :Output: PDB Distance as Temp
21+ [-o[utput]Dis[tance]2outDis2 (stdout ).as(outFile ) ] :Optional :Output: Distance List for Ca
22+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
23+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
24+>>>> Input and Reference File Format<<<<
25+ResidueNumberToBeFitted
26+...
27+If |, all residules are sellected till the residue in the next line
28+</PRE>
29+</BODY>
30+</HTML>
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