「参照付投影角度決定」の版間の差分
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== Eosによる実現方法 == | == Eosによる実現方法 == | ||
− | + | 演習では、Eosをつかった3次元再構成法の一例を示しています。下記に利用したMakefileを示します。 | |
+ | |||
+ | <pre> | ||
+ | # | ||
+ | # Eos for 3D reconstrucion from 2D rois using 3D initail reference | ||
+ | # | ||
+ | |||
+ | .SUFFIXES: .3d .ref3d .ref2d .pad .padtmp .mask .maskfit .fit .fitmask .roi .corinfo .3dinfo .3dlst .3d .3dsm .3dsmCenter .ds6 .3dsmds6 .corinfo2 .corinfolst .cormap .parcorinfolst .parcorinfolstsort .gnuplotcorinfolst .3dlstselect .monlst .mon | ||
+ | |||
+ | SHELL=/bin/bash | ||
+ | |||
+ | -include ROIs | ||
+ | -include CORINFOs | ||
+ | -include PADs | ||
+ | -include 3DINFOs | ||
+ | -include 3DLIST | ||
+ | -include CORINFO2s | ||
+ | |||
+ | # | ||
+ | # Initial Reference Model | ||
+ | INITIAL=initial | ||
+ | # Target structure name | ||
+ | TARGET=all | ||
+ | |||
+ | # Simultaneous Jobs for AutoRotaionCorrelation | ||
+ | JOP_NUM=-j 3 | ||
+ | |||
+ | # | ||
+ | # Search Area for 3D | ||
+ | # | ||
+ | ROTMODE=YOYS | ||
+ | # Rot1 | ||
+ | ROT1MIN=0 | ||
+ | ROT1MAX=359 | ||
+ | ROT1D=30 | ||
+ | nRot1=12 | ||
+ | # | ||
+ | ROT2MIN=0 | ||
+ | ROT2MAX=359 | ||
+ | ROT2D=30 | ||
+ | nRot2=12 | ||
+ | # Rot3 | ||
+ | ROT3MIN=0 | ||
+ | ROT3MAX=0 | ||
+ | ROT3D=30 | ||
+ | nRot3=1 | ||
+ | # For 2D | ||
+ | STEP=12 | ||
+ | ROTMIN=0 | ||
+ | ROTMAX=359 | ||
+ | nROT=`echo "" | awk 'BEGIN {printf 360 / $(STEP)}'` | ||
+ | |||
+ | # Seletion Step | ||
+ | COR_THRESHOLD=0.4 | ||
+ | Y_SHIFT_THRESHOLD=20 | ||
+ | |||
+ | # Pad size for 2D | ||
+ | PAD_W=64 | ||
+ | PAD_H=64 | ||
+ | |||
+ | ### | ||
+ | ### Initial model from PDB | ||
+ | ### | ||
+ | REFSOURCE=121p-shift | ||
+ | DELTA=2.5 | ||
+ | SIZE_X=64 | ||
+ | SIZE_Y=64 | ||
+ | SIZE_Z=64 | ||
+ | START_X=`awk 'BEGIN { print -1*$(DELTA)*$(SIZE_X)/2}'` | ||
+ | START_Y=`awk 'BEGIN { print -1*$(DELTA)*$(SIZE_Y)/2}'` | ||
+ | START_Z=`awk 'BEGIN { print -1*$(DELTA)*$(SIZE_Z)/2}'` | ||
+ | SNRATIO=3 | ||
+ | ############################### | ||
+ | |||
+ | Help:: | ||
+ | @echo "----- Makefile for Single Particle with Reference" | ||
+ | @echo "1. Prepare files from EM images, which has a suffix of roi " | ||
+ | @echo "2. Prepare an initial model as $(INITIAL).3d " | ||
+ | @echo "3. make First" | ||
+ | @echo "4. make All" | ||
+ | @echo "If you want to repeat refinement again, " | ||
+ | @echo " 1. make Again" | ||
+ | @echo " 2. make All" | ||
+ | @echo "" | ||
+ | @echo "--- If you want to create an initail model from PDB ---" | ||
+ | @echo " make InitialModel" | ||
+ | @echo "" | ||
+ | @echo "--- If you want to create an test from the initial model ---" | ||
+ | @echo " make TestData" | ||
+ | |||
+ | pad:$(ROIs:.roi=.pad) | ||
+ | corinfo:$(PADs:.pad=.corinfo) | ||
+ | 3dinfo:$(CORINFOs:.corinfo=.3dinfo) | ||
+ | fit:$(ROIs:.roi=.fit) | ||
+ | 3dlst:$(3DINFOs:.3dinfo=.3dlst) | ||
+ | 3d:$(3DLIST:.3dlst=.3d) | ||
+ | corinfo2:$(CORINFOs:.corinfo=.corinfo2) | ||
+ | parcorinfolst:$(CORINFO2s:.corinfo2=.parcorinfolst) | ||
+ | |||
+ | # | ||
+ | # | ||
+ | # | ||
+ | InitialModel:: | ||
+ | pdb2mrc -i $(REFSOURCE).pdb -o $(INITIAL).3d -nx $(SIZE_X) -ny $(SIZE_Y) -nz $(SIZE_Z) -Sx $(START_X) -Sy $(START_Y) -Sz $(START_Z) -dx $(DELTA) -dy $(DELTA) -dz $(DELTA) -m 1 | ||
+ | |||
+ | TestData:: | ||
+ | @for (( rot1 = $(ROT1MIN); rot1 <= $(ROT1MAX); rot1 += $(ROT1D)*2 )) \ | ||
+ | do \ | ||
+ | for (( rot2 = $(ROT2MIN); rot2 <= $(ROT2MAX); rot2 += $(ROT2D)*2 )) \ | ||
+ | do \ | ||
+ | for (( rot3 = $(ROT3MIN); rot3 <= $(ROT3MAX); rot3 += $(ROT3D)*2 )) \ | ||
+ | do \ | ||
+ | echo $$rot1, $$rot2, $$rot3; \ | ||
+ | mrc3Dto2D -i $(INITIAL).3d -o $(REFSOURCE)-$$rot1-$$rot2-$$rot3.roi \ | ||
+ | -InterpolationMode 2 -EulerMode $(ROTMODE) \ | ||
+ | -Rot1 $$rot1 $$rot1 1 \ | ||
+ | -Rot2 $$rot2 $$rot2 1 \ | ||
+ | -Rot3 $$rot3 $$rot3 1 ; \ | ||
+ | done \ | ||
+ | done \ | ||
+ | done | ||
+ | |||
+ | TestDataNoise:: | ||
+ | @for (( rot1 = $(ROT1MIN); rot1 <= $(ROT1MAX); rot1 += $(ROT1D)*2 )) \ | ||
+ | do \ | ||
+ | for (( rot2 = $(ROT2MIN); rot2 <= $(ROT2MAX); rot2 += $(ROT2D)*2 )) \ | ||
+ | do \ | ||
+ | for (( rot3 = $(ROT3MIN); rot3 <= $(ROT3MAX); rot3 += $(ROT3D)*2 )) \ | ||
+ | do \ | ||
+ | echo $$rot1, $$rot2, $$rot3; \ | ||
+ | name="$(REFSOURCE)-noise-$$rot1-$$rot2-$$rot3.roi"; \ | ||
+ | mrc3Dto2D -i $(INITIAL).3d -o $$name.noNoise \ | ||
+ | -InterpolationMode 2 -EulerMode $(ROTMODE) \ | ||
+ | -Rot1 $$rot1 $$rot1 1 \ | ||
+ | -Rot2 $$rot2 $$rot2 1 \ | ||
+ | -Rot3 $$rot3 $$rot3 1 ; \ | ||
+ | mrcImageNoiseAdd -i $$name.noNoise -o $$name -SN $(SNRATIO) ; \ | ||
+ | rm $$name.noNoise ; \ | ||
+ | done \ | ||
+ | done \ | ||
+ | done | ||
+ | |||
+ | ############## | ||
+ | ROIs:: | ||
+ | touch ROIs | ||
+ | echo "ROIs=\\" > ROIs | ||
+ | #find -name "*.roi" -type f | sed s/..// | xargs ls -1 | sed s/roi/roi\\\\/ >> ROIs | ||
+ | ls -1 *.roi | sed s/roi/roi\\\\/ >> ROIs | ||
+ | echo "" >> ROIs | ||
+ | |||
+ | CORINFOs:: | ||
+ | touch CORINFOs | ||
+ | echo "CORINFOs=\\" > CORINFOs | ||
+ | #find -name "*.corinfo" -type f | sed s/..// | xargs ls -1 | sed s/corinfo/corinfo\\\\/ >> CORINFOs | ||
+ | ls -1 *.corinfo | sed s/corinfo/corinfo\\\\/ >> CORINFOs | ||
+ | echo "" >> CORINFOs | ||
+ | |||
+ | PADs:: | ||
+ | touch PADs | ||
+ | echo "PADs=\\" > PADs | ||
+ | #find -name "*.pad" -type f | sed s/..// | xargs ls -1 | sed s/pad/pad\\\\/ >> PADs | ||
+ | ls -1 *.pad | sed s/pad/pad\\\\/ >> PADs | ||
+ | echo "" >> PADs | ||
+ | |||
+ | 3DINFOs:: | ||
+ | touch 3DINFOs | ||
+ | echo "3DINFOs=\\" > 3DINFOs | ||
+ | #find -name "*.3dinfo" -type f | sed s/..// | xargs ls -1 | sed s/3dinfo/3dinfo\\\\/ >> 3DINFOs | ||
+ | ls -1 *.3dinfo | sed s/3dinfo/3dinfo\\\\/ >> 3DINFOs | ||
+ | echo "" >> 3DINFOs | ||
+ | |||
+ | 3DLIST:: | ||
+ | touch 3DLIST | ||
+ | echo "3DLIST=\\" > 3DLIST | ||
+ | #find -name "*.3dlst" -type f | sed s/..// | xargs ls -1 | sed s/3dlst/3dlst\\\\/ >> 3DLIST | ||
+ | ls -1 *.3dlst | sed s/3dlst/3dlst\\\\/ >> 3DLIST | ||
+ | echo "" >> 3DLIST | ||
+ | |||
+ | CORINFO2s:: | ||
+ | touch CORINFO2s | ||
+ | echo "CORINFO2s=\\" > CORINFO2s | ||
+ | #find -name "*.corinfo2" -type f | sed s/..// | xargs ls -1 | sed s/corinfo2/corinfo2\\\\/ >> CORINFO2s | ||
+ | ls -1 *.corinfo2 | sed s/corinfo2/corinfo2\\\\/ >> CORINFO2s | ||
+ | echo "" >> CORINFO2s | ||
+ | |||
+ | ############## | ||
+ | First:: | ||
+ | cp $(INITIAL).3d $(TARGET).ref3d | ||
+ | touch *.roi | ||
+ | |||
+ | All:: | ||
+ | make $(TARGET).ref2d; | ||
+ | make ROIs; | ||
+ | make $(JOP_NUM) pad; | ||
+ | make PADs; | ||
+ | make $(JOP_NUM) corinfo; | ||
+ | make CORINFOs; | ||
+ | make $(JOP_NUM) 3dinfo; | ||
+ | make 3DINFOs; | ||
+ | make $(JOP_NUM) 3dlst; | ||
+ | make 3DLIST; | ||
+ | make $(TARGET).3d; | ||
+ | |||
+ | Again:: | ||
+ | touch *.pad | ||
+ | cp $(TARGET).3d $(TARGET).ref3d; | ||
+ | TMPNAME=`date +%y%m%d%H%M%S`; \ | ||
+ | mv $(TARGET).3dlst $(TARGET).3dlst.$$TMPNAME; \ | ||
+ | mv $(TARGET).3d $(TARGET).3d.$$TMPNAME; \ | ||
+ | mv $(TARGET).3dsm $(TARGET).3dsm.$$TMPNAME; \ | ||
+ | mv $(TARGET).ds6 $(TARGET).ds6.$$TMPNAME; \ | ||
+ | mv $(TARGET).3dsmds6 $(TARGET).3dsmds6.$$TMPNAME; | ||
+ | |||
+ | |||
+ | #### Prepare Reference #### | ||
+ | |||
+ | .ref3d.ref2d: | ||
+ | mrc3Dto2D -i $(TARGET).ref3d -o $(TARGET).ref2d -EulerMode $(ROTMODE) -InterpolationMode 2 -Rot2 $(ROT2MIN) $(ROT2MAX) $(ROT2D) -Rot1 $(ROT1MIN) $(ROT1MAX) $(ROT1D) -Rot3 $(ROT3MIN) $(ROT3MAX) $(ROT3D) -m 0 | ||
+ | |||
+ | .roi.pad: | ||
+ | mrcImageWindowing -i $*.roi -o $*.mask -W 0.1 0.0 0.05 0.0 -m 18 | ||
+ | mrcImagePad -i $*.mask -o $*.padtmp -W $(PAD_W) -H $(PAD_H) -m 3 | ||
+ | mrcImageWindowing -i $*.padtmp -o $*.pad -W 0.1 0.0 0.1 0.0 -m 2 | ||
+ | |||
+ | .pad.corinfo: | ||
+ | mrcImageAutoRotationCorrelation -i $*.pad -r $(TARGET).ref2d -O $*.corinfo -fit $*.fit -cor $*.cormap -n $(nRot) -m 18 -range $(ROTMIN) $(ROTMAX) -Iter 2 -nRot2 $(nRot2) -nRot1 $(nRot1) -nRot3 $(nRot3) 2> /dev/null | ||
+ | |||
+ | ############################################################################## | ||
+ | |||
+ | |||
+ | .corinfo.3dinfo: | ||
+ | awk '/Cor/ { print $$7,$$16,$$2,$$3,$$4,$$5,$$9,$$11,$$12}' $*.corinfo | sort -r | sed -e s/.pad/.fit/ > $*.3dinfolst | ||
+ | head -n 1 $*.3dinfolst | awk '{print $$2,$$3,$$4,$$5,$$6,$$1}' > $*.3dinfo | ||
+ | ## ##18 -> ##7 ## | ||
+ | |||
+ | .3dinfo.3dlst: | ||
+ | cat $*.3dinfo >> $(TARGET).3dlst | ||
+ | |||
+ | .3dlst.3d: | ||
+ | mrc2Dto3D -I $(TARGET).3dlst -o $(TARGET).3d -InterpolationMode 2 -Double -DoubleCounter $(TARGET).3dcounter -CounterThreshold 0.5 -m 1 -WeightMode 2 | ||
+ | |||
+ | .3d.3dsm: | ||
+ | mrcImageSmoothing -i $(TARGET).3d -o $(TARGET).3dsm -m 1 -M 1 -r 3 | ||
+ | |||
+ | .3dsm.3dsmCenter: | ||
+ | mrcImageCenterGet -i $(TARGET).3dsm -o $(TARGET).3dsmCenter -Nx 128 -Ny 128 -Nz 128 | ||
+ | |||
+ | .3dsmCenter.ds6: | ||
+ | mrc2map -i $(TARGET).3dsmCenter -o $(TARGET).ds6 -m 3 | ||
+ | |||
+ | .3d.ds6: | ||
+ | mrc2map -i $*.3d -o $*.ds6 -m 0 | ||
+ | |||
+ | #####Select Particles##### | ||
+ | |||
+ | .corinfo.corinfo2: | ||
+ | awk '/Cor/ { print $$18,$$16,$$2,$$3,$$4,$$5,$$9,$$11,$$12}' $*.corinfo | sort -r | sed -e 's/.roi/.fit/' > $*.corinfolst | ||
+ | head -n 1 $*.corinfolst | awk '{if($(PAD_W)-$$8>=$$8&&$(PAD_H)-$$9>=$$9) print $$1,$$2,$$3,$$4,$$5,$$6,$$7,0+$$8,0+$$9;else if($(PAD_W)-$$8>=$$8) print $$1,$$2,$$3,$$4,$$5,$$6,$$7,0+$$8,$(PAD_H)-$$9;else if($(PAD_H)-$$9>=$$9) print $$1,$$2,$$3,$$4,$$5,$$6,$$7,$(PAD_W)-$$8,0+$$9;else print $$1,$$2,$$3,$$4,$$5,$$6,$$7,$(PAD_W)-$$8,$(PAD_H)-$$9}' > $*.corinfo2 | ||
+ | |||
+ | .corinfo2.parcorinfolst: | ||
+ | cat $*.corinfo2 >> $(TARGET).parcorinfolst | ||
+ | |||
+ | CorinfoSort:: | ||
+ | awk '{ print $$1,$$2,$$3,$$4,$$5,$$6,$$7,$$8,$$9}' $(TARGET).parcorinfolst | sort -r > $(TARGET).parcorinfolstsort | ||
+ | |||
+ | SelectParticle:: | ||
+ | awk '$$1 >= $(COR_THRESHOLD) || $$9 <= $(Y_SHIFT_THRESHOLD){print $$2,$$3,$$4,$$5,$$6,$$1}' $(TARGET).parcorinfolstsort > $(TARGET).3dlstselect | ||
+ | |||
+ | |||
+ | #####Check alignment##### | ||
+ | |||
+ | GnuplotCorinfo:: | ||
+ | awk '{ print $$1,$$9}' $(TARGET).parcorinfolst | sort -r > $(TARGET).gnuplotcorinfolst | ||
+ | #################################################### | ||
+ | ##gnuplot | ||
+ | ##set out "Corinfo.ps" | ||
+ | ##plot "$(TARGET).gnuplotcorinfolst" | ||
+ | ################################################### | ||
+ | |||
+ | GnuplotAngle:: | ||
+ | awk '{ print $$4,$$5}' $(TARGET).parcorinfolst > $(TARGET).gnuplotanglelst | ||
+ | ###################################################### | ||
+ | ##gnuplot | ||
+ | ##set out "Angle.ps" | ||
+ | ##plot "$(TARGET).gnuplotanglelst" | ||
+ | ###################################################### | ||
+ | |||
+ | GnuplotShift:: | ||
+ | awk '{ print $$4,$$5}' $(TARGET).parcorinfolst > $(TARGET).gnuplotshiftlst | ||
+ | ###################################################### | ||
+ | ##gnuplot | ||
+ | ##set out "Shift.ps" | ||
+ | ##plot "$(TARGET).gnuplotshiftlst" | ||
+ | ###################################################### | ||
+ | |||
+ | MontageList:: | ||
+ | awk '{ print $$1}' $(TARGET).3dlst > $(TARGET).monlst | ||
+ | mrcImageMontageCreate -i $(TARGET).monlst -o $(TARGET).mon -nx 15 -ny 10 | ||
+ | |||
+ | </pre> |
2012年9月28日 (金) 20:25時点における版
参照付投影角度の決定のためには、参照像が必要です。手順を下記に述べます。
1.参照像(3次元)を準備する
2.参照像(2次元)を3次元像から参照投影像として作成する。それぞれの参照投影像は角度が決定されています。
3.切り出した2次元投影画像と2で作成した参照投影像とを比較して、一番似ている参照投影像を選択し、それぞれの2次元画像の投影角として推定します。その際、参照画像に一番適合した位置、回転方向に投影像を回転及び移動し、3次元再構成のための投影像のセットを手に入れいます。
4.推定した投影角を用いて、3次元再構成のための投影像のセットから3次元再構成を行います。
似ている画像の決定方法
最も利用されるのは、相関関数を用いた方法です。この相関関数の前処理等を行い、ノイズによる影響を抑えることで、よりよい相関を得るように工夫が必要です。 相関関数そのものも今後更に検討が必要だと思います。
Eosによる実現方法
演習では、Eosをつかった3次元再構成法の一例を示しています。下記に利用したMakefileを示します。
# # Eos for 3D reconstrucion from 2D rois using 3D initail reference # .SUFFIXES: .3d .ref3d .ref2d .pad .padtmp .mask .maskfit .fit .fitmask .roi .corinfo .3dinfo .3dlst .3d .3dsm .3dsmCenter .ds6 .3dsmds6 .corinfo2 .corinfolst .cormap .parcorinfolst .parcorinfolstsort .gnuplotcorinfolst .3dlstselect .monlst .mon SHELL=/bin/bash -include ROIs -include CORINFOs -include PADs -include 3DINFOs -include 3DLIST -include CORINFO2s # # Initial Reference Model INITIAL=initial # Target structure name TARGET=all # Simultaneous Jobs for AutoRotaionCorrelation JOP_NUM=-j 3 # # Search Area for 3D # ROTMODE=YOYS # Rot1 ROT1MIN=0 ROT1MAX=359 ROT1D=30 nRot1=12 # ROT2MIN=0 ROT2MAX=359 ROT2D=30 nRot2=12 # Rot3 ROT3MIN=0 ROT3MAX=0 ROT3D=30 nRot3=1 # For 2D STEP=12 ROTMIN=0 ROTMAX=359 nROT=`echo "" | awk 'BEGIN {printf 360 / $(STEP)}'` # Seletion Step COR_THRESHOLD=0.4 Y_SHIFT_THRESHOLD=20 # Pad size for 2D PAD_W=64 PAD_H=64 ### ### Initial model from PDB ### REFSOURCE=121p-shift DELTA=2.5 SIZE_X=64 SIZE_Y=64 SIZE_Z=64 START_X=`awk 'BEGIN { print -1*$(DELTA)*$(SIZE_X)/2}'` START_Y=`awk 'BEGIN { print -1*$(DELTA)*$(SIZE_Y)/2}'` START_Z=`awk 'BEGIN { print -1*$(DELTA)*$(SIZE_Z)/2}'` SNRATIO=3 ############################### Help:: @echo "----- Makefile for Single Particle with Reference" @echo "1. Prepare files from EM images, which has a suffix of roi " @echo "2. Prepare an initial model as $(INITIAL).3d " @echo "3. make First" @echo "4. make All" @echo "If you want to repeat refinement again, " @echo " 1. make Again" @echo " 2. make All" @echo "" @echo "--- If you want to create an initail model from PDB ---" @echo " make InitialModel" @echo "" @echo "--- If you want to create an test from the initial model ---" @echo " make TestData" pad:$(ROIs:.roi=.pad) corinfo:$(PADs:.pad=.corinfo) 3dinfo:$(CORINFOs:.corinfo=.3dinfo) fit:$(ROIs:.roi=.fit) 3dlst:$(3DINFOs:.3dinfo=.3dlst) 3d:$(3DLIST:.3dlst=.3d) corinfo2:$(CORINFOs:.corinfo=.corinfo2) parcorinfolst:$(CORINFO2s:.corinfo2=.parcorinfolst) # # # InitialModel:: pdb2mrc -i $(REFSOURCE).pdb -o $(INITIAL).3d -nx $(SIZE_X) -ny $(SIZE_Y) -nz $(SIZE_Z) -Sx $(START_X) -Sy $(START_Y) -Sz $(START_Z) -dx $(DELTA) -dy $(DELTA) -dz $(DELTA) -m 1 TestData:: @for (( rot1 = $(ROT1MIN); rot1 <= $(ROT1MAX); rot1 += $(ROT1D)*2 )) \ do \ for (( rot2 = $(ROT2MIN); rot2 <= $(ROT2MAX); rot2 += $(ROT2D)*2 )) \ do \ for (( rot3 = $(ROT3MIN); rot3 <= $(ROT3MAX); rot3 += $(ROT3D)*2 )) \ do \ echo $$rot1, $$rot2, $$rot3; \ mrc3Dto2D -i $(INITIAL).3d -o $(REFSOURCE)-$$rot1-$$rot2-$$rot3.roi \ -InterpolationMode 2 -EulerMode $(ROTMODE) \ -Rot1 $$rot1 $$rot1 1 \ -Rot2 $$rot2 $$rot2 1 \ -Rot3 $$rot3 $$rot3 1 ; \ done \ done \ done TestDataNoise:: @for (( rot1 = $(ROT1MIN); rot1 <= $(ROT1MAX); rot1 += $(ROT1D)*2 )) \ do \ for (( rot2 = $(ROT2MIN); rot2 <= $(ROT2MAX); rot2 += $(ROT2D)*2 )) \ do \ for (( rot3 = $(ROT3MIN); rot3 <= $(ROT3MAX); rot3 += $(ROT3D)*2 )) \ do \ echo $$rot1, $$rot2, $$rot3; \ name="$(REFSOURCE)-noise-$$rot1-$$rot2-$$rot3.roi"; \ mrc3Dto2D -i $(INITIAL).3d -o $$name.noNoise \ -InterpolationMode 2 -EulerMode $(ROTMODE) \ -Rot1 $$rot1 $$rot1 1 \ -Rot2 $$rot2 $$rot2 1 \ -Rot3 $$rot3 $$rot3 1 ; \ mrcImageNoiseAdd -i $$name.noNoise -o $$name -SN $(SNRATIO) ; \ rm $$name.noNoise ; \ done \ done \ done ############## ROIs:: touch ROIs echo "ROIs=\\" > ROIs #find -name "*.roi" -type f | sed s/..// | xargs ls -1 | sed s/roi/roi\\\\/ >> ROIs ls -1 *.roi | sed s/roi/roi\\\\/ >> ROIs echo "" >> ROIs CORINFOs:: touch CORINFOs echo "CORINFOs=\\" > CORINFOs #find -name "*.corinfo" -type f | sed s/..// | xargs ls -1 | sed s/corinfo/corinfo\\\\/ >> CORINFOs ls -1 *.corinfo | sed s/corinfo/corinfo\\\\/ >> CORINFOs echo "" >> CORINFOs PADs:: touch PADs echo "PADs=\\" > PADs #find -name "*.pad" -type f | sed s/..// | xargs ls -1 | sed s/pad/pad\\\\/ >> PADs ls -1 *.pad | sed s/pad/pad\\\\/ >> PADs echo "" >> PADs 3DINFOs:: touch 3DINFOs echo "3DINFOs=\\" > 3DINFOs #find -name "*.3dinfo" -type f | sed s/..// | xargs ls -1 | sed s/3dinfo/3dinfo\\\\/ >> 3DINFOs ls -1 *.3dinfo | sed s/3dinfo/3dinfo\\\\/ >> 3DINFOs echo "" >> 3DINFOs 3DLIST:: touch 3DLIST echo "3DLIST=\\" > 3DLIST #find -name "*.3dlst" -type f | sed s/..// | xargs ls -1 | sed s/3dlst/3dlst\\\\/ >> 3DLIST ls -1 *.3dlst | sed s/3dlst/3dlst\\\\/ >> 3DLIST echo "" >> 3DLIST CORINFO2s:: touch CORINFO2s echo "CORINFO2s=\\" > CORINFO2s #find -name "*.corinfo2" -type f | sed s/..// | xargs ls -1 | sed s/corinfo2/corinfo2\\\\/ >> CORINFO2s ls -1 *.corinfo2 | sed s/corinfo2/corinfo2\\\\/ >> CORINFO2s echo "" >> CORINFO2s ############## First:: cp $(INITIAL).3d $(TARGET).ref3d touch *.roi All:: make $(TARGET).ref2d; make ROIs; make $(JOP_NUM) pad; make PADs; make $(JOP_NUM) corinfo; make CORINFOs; make $(JOP_NUM) 3dinfo; make 3DINFOs; make $(JOP_NUM) 3dlst; make 3DLIST; make $(TARGET).3d; Again:: touch *.pad cp $(TARGET).3d $(TARGET).ref3d; TMPNAME=`date +%y%m%d%H%M%S`; \ mv $(TARGET).3dlst $(TARGET).3dlst.$$TMPNAME; \ mv $(TARGET).3d $(TARGET).3d.$$TMPNAME; \ mv $(TARGET).3dsm $(TARGET).3dsm.$$TMPNAME; \ mv $(TARGET).ds6 $(TARGET).ds6.$$TMPNAME; \ mv $(TARGET).3dsmds6 $(TARGET).3dsmds6.$$TMPNAME; #### Prepare Reference #### .ref3d.ref2d: mrc3Dto2D -i $(TARGET).ref3d -o $(TARGET).ref2d -EulerMode $(ROTMODE) -InterpolationMode 2 -Rot2 $(ROT2MIN) $(ROT2MAX) $(ROT2D) -Rot1 $(ROT1MIN) $(ROT1MAX) $(ROT1D) -Rot3 $(ROT3MIN) $(ROT3MAX) $(ROT3D) -m 0 .roi.pad: mrcImageWindowing -i $*.roi -o $*.mask -W 0.1 0.0 0.05 0.0 -m 18 mrcImagePad -i $*.mask -o $*.padtmp -W $(PAD_W) -H $(PAD_H) -m 3 mrcImageWindowing -i $*.padtmp -o $*.pad -W 0.1 0.0 0.1 0.0 -m 2 .pad.corinfo: mrcImageAutoRotationCorrelation -i $*.pad -r $(TARGET).ref2d -O $*.corinfo -fit $*.fit -cor $*.cormap -n $(nRot) -m 18 -range $(ROTMIN) $(ROTMAX) -Iter 2 -nRot2 $(nRot2) -nRot1 $(nRot1) -nRot3 $(nRot3) 2> /dev/null ############################################################################## .corinfo.3dinfo: awk '/Cor/ { print $$7,$$16,$$2,$$3,$$4,$$5,$$9,$$11,$$12}' $*.corinfo | sort -r | sed -e s/.pad/.fit/ > $*.3dinfolst head -n 1 $*.3dinfolst | awk '{print $$2,$$3,$$4,$$5,$$6,$$1}' > $*.3dinfo ## ##18 -> ##7 ## .3dinfo.3dlst: cat $*.3dinfo >> $(TARGET).3dlst .3dlst.3d: mrc2Dto3D -I $(TARGET).3dlst -o $(TARGET).3d -InterpolationMode 2 -Double -DoubleCounter $(TARGET).3dcounter -CounterThreshold 0.5 -m 1 -WeightMode 2 .3d.3dsm: mrcImageSmoothing -i $(TARGET).3d -o $(TARGET).3dsm -m 1 -M 1 -r 3 .3dsm.3dsmCenter: mrcImageCenterGet -i $(TARGET).3dsm -o $(TARGET).3dsmCenter -Nx 128 -Ny 128 -Nz 128 .3dsmCenter.ds6: mrc2map -i $(TARGET).3dsmCenter -o $(TARGET).ds6 -m 3 .3d.ds6: mrc2map -i $*.3d -o $*.ds6 -m 0 #####Select Particles##### .corinfo.corinfo2: awk '/Cor/ { print $$18,$$16,$$2,$$3,$$4,$$5,$$9,$$11,$$12}' $*.corinfo | sort -r | sed -e 's/.roi/.fit/' > $*.corinfolst head -n 1 $*.corinfolst | awk '{if($(PAD_W)-$$8>=$$8&&$(PAD_H)-$$9>=$$9) print $$1,$$2,$$3,$$4,$$5,$$6,$$7,0+$$8,0+$$9;else if($(PAD_W)-$$8>=$$8) print $$1,$$2,$$3,$$4,$$5,$$6,$$7,0+$$8,$(PAD_H)-$$9;else if($(PAD_H)-$$9>=$$9) print $$1,$$2,$$3,$$4,$$5,$$6,$$7,$(PAD_W)-$$8,0+$$9;else print $$1,$$2,$$3,$$4,$$5,$$6,$$7,$(PAD_W)-$$8,$(PAD_H)-$$9}' > $*.corinfo2 .corinfo2.parcorinfolst: cat $*.corinfo2 >> $(TARGET).parcorinfolst CorinfoSort:: awk '{ print $$1,$$2,$$3,$$4,$$5,$$6,$$7,$$8,$$9}' $(TARGET).parcorinfolst | sort -r > $(TARGET).parcorinfolstsort SelectParticle:: awk '$$1 >= $(COR_THRESHOLD) || $$9 <= $(Y_SHIFT_THRESHOLD){print $$2,$$3,$$4,$$5,$$6,$$1}' $(TARGET).parcorinfolstsort > $(TARGET).3dlstselect #####Check alignment##### GnuplotCorinfo:: awk '{ print $$1,$$9}' $(TARGET).parcorinfolst | sort -r > $(TARGET).gnuplotcorinfolst #################################################### ##gnuplot ##set out "Corinfo.ps" ##plot "$(TARGET).gnuplotcorinfolst" ################################################### GnuplotAngle:: awk '{ print $$4,$$5}' $(TARGET).parcorinfolst > $(TARGET).gnuplotanglelst ###################################################### ##gnuplot ##set out "Angle.ps" ##plot "$(TARGET).gnuplotanglelst" ###################################################### GnuplotShift:: awk '{ print $$4,$$5}' $(TARGET).parcorinfolst > $(TARGET).gnuplotshiftlst ###################################################### ##gnuplot ##set out "Shift.ps" ##plot "$(TARGET).gnuplotshiftlst" ###################################################### MontageList:: awk '{ print $$1}' $(TARGET).3dlst > $(TARGET).monlst mrcImageMontageCreate -i $(TARGET).monlst -o $(TARGET).mon -nx 15 -ny 10