def computeAtomShifts(log,WorkingDir,NumberOfModes):
fnOutDir=os.path.join(WorkingDir,"extra/distanceProfiles")
createDir(log,fnOutDir)
maxShift=[]
maxShiftMode=[]
for n in range(7,NumberOfModes+1):
fhIn=open(os.path.join(WorkingDir,"modes/vec."+str(n)))
md=MetaData()
atomCounter=0;
for line in fhIn:
coord=line.split()
x=float(coord[0])
y=float(coord[1])
z=float(coord[2])
d=math.sqrt(x*x+y*y+z*z)
if n==7:
maxShift.append(d)
maxShiftMode.append(7)
else:
if d>maxShift[atomCounter]:
maxShift[atomCounter]=d
maxShiftMode[atomCounter]=n
atomCounter+=1
md.setValue(MDL_NMA_ATOMSHIFT,d,md.addObject())
md.write(os.path.join(fnOutDir,"vec"+str(n)+".xmd"))
fhIn.close()
md=MetaData()
for i in range(len(maxShift)):
id=md.addObject()
md.setValue(MDL_NMA_ATOMSHIFT,maxShift[i],id)
md.setValue(MDL_NMA_MODEFILE,os.path.join(WorkingDir,"modes/vec."+str(maxShiftMode[i]+1)),id)
md.write(os.path.join(WorkingDir,'extra','maxAtomShifts.xmd'))
def animateModes(log,WorkingDir,LastMode,Amplitude,NFrames,Downsample,PseudoAtomThreshold,PseudoAtomRadius,Sampling,StructureType):
createDir(log,os.path.join(WorkingDir,"extra/animations"))
currentDir=os.getcwd()
changeDir(log,WorkingDir)
if StructureType=="EM":
fn="pseudoatoms.pdb"
runJob(log,"nma_animate_pseudoatoms.py","%s extra/vec_ani.pkl 7 %d %f extra/animations/animated_mode %d %d %f"%\
(fn,LastMode,Amplitude,NFrames,Downsample,PseudoAtomThreshold))
else:
fn="atoms.pdb"
runJob(log,"nma_animate_atoms.py","%s extra/vec_ani.pkl 7 %d %f extra/animations/animated_mode %d"%\
(fn,LastMode,Amplitude,NFrames))
for mode in range(7,LastMode+1):
fnAnimation="extra/animations/animated_mode_%03d"%mode
fhCmd=open(fnAnimation+".vmd",'w')
fhCmd.write("mol new "+os.path.join(WorkingDir,fnAnimation)+".pdb\n")
fhCmd.write("animate style Loop\n")
fhCmd.write("display projection Orthographic\n")
if StructureType=="EM":
fhCmd.write("mol modcolor 0 0 Beta\n")
fhCmd.write("mol modstyle 0 0 Beads %f 8.000000\n"%(PseudoAtomRadius*Sampling))
else:
fhCmd.write("mol modcolor 0 0 Index\n")
fhCmd.write("mol modstyle 0 0 Beads 1.000000 8.000000\n")
fhCmd.write("animate speed 0.5\n")
fhCmd.write("animate forward\n")
fhCmd.close();
changeDir(log,currentDir)
def reformatOutputPDB(log,WorkingDir,NumberOfModes):
currentDir=os.getcwd()
changeDir(log,WorkingDir)
createDir(log,"modes")
Natoms=countAtoms("atoms.pdb")
fhIn=open('diagrtb.eigenfacs')
fhAni=open('vec_ani.txt','w')
for n in range(NumberOfModes):
# Skip two lines
fhIn.readline()
fhIn.readline()
fhOut=open('modes/vec.%d'%(n+1),'w')
for i in range(Natoms):
line=fhIn.readline()
fhOut.write(line)
fhAni.write(line.rstrip().lstrip()+" ")
fhOut.close()
if n!=(NumberOfModes-1):
fhAni.write("\n")
fhIn.close()
fhAni.close()
runJob(log,"nma_prepare_for_animate.py","")
runJob(log,"rm","vec_ani.txt")
moveFile(log,'vec_ani.pkl','extra/vec_ani.pkl')
changeDir(log,currentDir)
def reformatOutput(log,WorkingDir):
currentDir=os.getcwd()
changeDir(log,WorkingDir)
Natoms=countAtoms("pseudoatoms.pdb")
runJob(log,"nma_reformat_vector_foranimate.pl","%d fort.11"%Natoms)
runJob(log,"cat","vec.1* > vec_ani.txt")
runJob(log,"rm","-f vec.1*")
runJob(log,"nma_reformat_vector.pl","%d fort.11"%Natoms)
createDir(log,"modes")
runJob(log,"mv","-f vec.* modes")
runJob(log,"nma_prepare_for_animate.py","")
runJob(log,"rm","vec_ani.txt fort.11 matrice.sdijf")
moveFile(log,'vec_ani.pkl','extra/vec_ani.pkl')
changeDir(log,currentDir)
def estimateSingleCTF(log, WorkingDir, inputFile, DownsampleFactor, AutomaticDownsampling,
Voltage, SphericalAberration, AngPix, AmplitudeContrast, LowResolCutoff,
HighResolCutoff,WinSize,MaxFocus,MinFocus,FastDefocus,MDL_TYPE):
extraDir=os.path.join(WorkingDir,'extra')
tmpDir=os.path.join(WorkingDir,'tmp')
micrographName = os.path.basename(inputFile)
shortname = os.path.splitext(micrographName)[0]
micrographDir = os.path.join(extraDir,shortname)
oroot="%s/xmipp_ctf"%micrographDir
if not os.path.exists(micrographDir):
createDir(log,micrographDir)
downsampleList=[DownsampleFactor]
if AutomaticDownsampling:
downsampleList.append(DownsampleFactor+1)
if DownsampleFactor>=2:
downsampleList.append(DownsampleFactor-1)
else:
downsampleList.append(max(DownsampleFactor/2.,1.))
for DownsampleFactor in downsampleList:
# Downsample if necessary
deleteTmp=False
if DownsampleFactor != 1:
finalname = os.path.join(tmpDir,shortname + "_tmp.mrc")
runJob(log,"xmipp_transform_downsample","-i %s -o %s --step %f --method fourier" % (inputFile,finalname,DownsampleFactor))
deleteTmp=True
else:
finalname = inputFile
# CTF estimation with Xmipp
args="--micrograph "+finalname+\
" --oroot "+oroot+\
" --kV "+str(Voltage)+\
" --Cs "+str(SphericalAberration)+\
" --sampling_rate "+str(AngPix*DownsampleFactor)+\
" --downSamplingPerformed "+str(DownsampleFactor)+\
" --ctfmodelSize 256"+\
" --Q0 "+str(AmplitudeContrast)+\
" --min_freq "+str(LowResolCutoff)+\
" --max_freq "+str(HighResolCutoff)+\
" --pieceDim "+str(WinSize)+\
" --defocus_range "+str((MaxFocus-MinFocus)*10000/2)+\
" --defocusU "+str((MaxFocus+MinFocus)*10000/2)
if (FastDefocus):
args+=" --fastDefocus"
runJob(log,'xmipp_ctf_estimate_from_micrograph', args)
if deleteTmp:
deleteFile(log, finalname)
md = xmipp.MetaData()
id = md.addObject()
if MDL_TYPE == xmipp.MDL_MICROGRAPH_MOVIE:
md.setValue(xmipp.MDL_MICROGRAPH_MOVIE,inputFile,id)
md.setValue(xmipp.MDL_MICROGRAPH,('%05d@%s'%(1,inputFile)),id)
else:
md.setValue(xmipp.MDL_MICROGRAPH,inputFile,id)
md.setValue(xmipp.MDL_PSD,oroot+".psd",id)
md.setValue(xmipp.MDL_PSD_ENHANCED,oroot+"_enhanced_psd.xmp",id)
md.setValue(xmipp.MDL_CTF_MODEL,oroot+".ctfparam",id)
md.setValue(xmipp.MDL_IMAGE1,oroot+"_ctfmodel_quadrant.xmp",id)
md.setValue(xmipp.MDL_IMAGE2,oroot+"_ctfmodel_halfplane.xmp",id)
md.setValue(xmipp.MDL_CTF_DOWNSAMPLE_PERFORMED,float(DownsampleFactor),id)
fnEval=os.path.join(micrographDir,"xmipp_ctf.xmd")
md.write(fnEval)
criterion="ctfCritFirstZero<5 OR ctfCritMaxFreq>20 OR ctfCritfirstZeroRatio<0.9 OR ctfCritfirstZeroRatio>1.1 OR "\
"ctfCritFirstMinFirstZeroRatio>10 OR ctfCritCorr13<0 OR ctfCritCtfMargin<0 OR ctfCritNonAstigmaticValidty<0.3 OR " \
"ctfCritNonAstigmaticValidty>25"
runJob(log,"xmipp_ctf_sort_psds","-i %s"%(fnEval))
fnRejected=os.path.join(tmpDir,shortname+"_rejected.xmd")
runJob(log,"xmipp_metadata_utilities",'-i %s --query select "%s" -o %s'%(fnEval,criterion,fnRejected))
md.read(fnRejected)
if md.size()==0:
break
def importTomogram(log, TomogramDir, TomogramRoot, params):
createDir(log, TomogramDir)
runJob(log, "xmipp_xray_import", params, NumberOfMpi=1)
