llExtractWithLayerSeparation
Usage
Usage: llExtractWithLayerSeparation
Options:
[-i[nput] In (NULL ).as(inFileListNoOpen ) ] :Essential :InputDataFile(mrcImage:Fourier Space)
[-I[nput] InLLNea (NULL ).as(inFileListNoOpen )
InLLFar (NULL ).as(inFileListNoOpen ) ] :Optional :InputDataFile(llData:Already separated)
[-r[ef] Ref (NULL ).as(inFile ) ] :Optional :ReferenceData(llData:Gnl(R) Space)
[-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile(llData: Average File)
[-o2[utput] Out2 (NULL ).as(outFileListNoOpen ) ] :Optional :OutputDataFileList(llData: Each Filament which has the same orientation as average)
[-o3[utput] Out3 (NULL ).as(outFileListNoOpen ) ] :Optional :OutputDataFileList(llData: Difference of each filament)
[-o4[utput] Out4 (NULL ).as(outFileListNoOpen ) ] :Optional :OutputDataFileList(llData: Each Filament which has the same orientaion as original filament)
[-o5[utput] Out5 (NULL ).as(outFileListNoOpen ) ] :Optional :OutputDataFileList(mrcImage: P-Value)
[-o6[utput] Out6 (NULL ).as(outFileListNoOpen ) ] :Optional :OutputDataFileList(mrcImage: Q-Value)
[-o7[utput] Out7 (NULL ).as(outFile ) ] :Optional :OutputDataFile(Text: Two subsets for resolution estimation)
[-o8[utput] Out8 (NULL ).as(outFile ) ] :Optional :OutputDataFile(Text: For Back Projection)
[-o9[utput] Out9 (NULL ).as(outFileListNoOpen ) ] :Optional :OutputDataFileList(Text: x shift, z shift and dY information)
[-comment InComment (NULL ).as(String ) ] :Optional :Comment
[-symmetry symmetry (1.0 ).as(Real ) ] :Optional :Symmetry for back projection text file
[-l[ayerInfo] llInfo (NULL ).as(inFileListNoOpen ) ] :Essential :LayerLineInformation
[-l[ayerInfo]final llInfoFinal (NULL ).as(inFile ) ] :Optional :LayerLineInformation(Final)
[-li[ayerInfo] llInfoImp (NULL ).as(inFileListNoOpen ) ] :Optional :LayerLineInformationImportant
[-liw[ayerInfo] liWeight (1.0 ).as(Real ) ] :Optional :Weight of Important Layer
[-liwStart[ayerInfo] liWeightStart (1.0 ).as(Real ) ] :Optional :Weight of Important Layer
[-liwStep[ayerInfo] liWeightStep (1.0 ).as(Real ) ] :Optional :Weight of Important Layer
[-la[ayerInfo] llInfoAxis (NULL ).as(inFileListNoOpen ) ] :Optional :LayerLineInformationForAxisSearch
[-law[ayerInfo] laWeight (1.0 ).as(Real ) ] :Optional :Weight of Important Layer for AS
[-lawStart[ayerInfo] laWeightStart (1.0 ).as(Real ) ] :Optional :Weight of Important Layer for AS
[-lawStep[ayerInfo] laWeightStep (1.0 ).as(Real ) ] :Optional :Weight of Important Layer for AS
[-truePitch truePitch (430.0 ).as(Real ) ] :Essential :true pitch [A]
[-rMax rMax (100.0 ).as(Real ) ] :Essential :rMax [A]
[-rMaxMin rMaxMin (100.0 ).as(Real ) ] :Optional :rMaxMin [A]
[-RMax RMax (0.1 ).as(Real ) ] :Optional :RMax [/A]
[-RMaxFirst RMaxFirst (0.04 ).as(Real ) ] :Optional :RMaxFirst [/A]: Def: RMax
[-RMaxStep RMaxStep (0.02 ).as(Real ) ] :Optional :RMaxStep [/A]
[-RRMax RRMax (0.1 ).as(Real ) ] :Optional :Radial RMax [/A]
[-RRMaxFirst RRMaxFirst (0.04 ).as(Real ) ] :Optional :Radial RMaxFirst [/A]: Def: RMax
[-RRMaxStep RRMaxStep (0.02 ).as(Real ) ] :Optional :Radial RMaxStep [/A]
[-delBR delBR (0.0002 ).as(Real ) ] :Optional :delBR [/A]
[-rms rms (1e-6 ).as(Real ) ] :Optional :rms:
[-narrowSearch narrowSearch (1.0 ).as(Real ) ] :Optional :narrowSearch[Degree]: P-Value and Q-Value
[-nextTimes nextTimes (1e-4 ).as(Real ) ] :Optional :nextTimes: rms
[-maxIter[ation] MaxIteration (10 ).as(Integer ) ] :Optional :max iteration:
[-maxIter2[ation] MaxIter2 (1 ).as(Integer ) ] :Optional :max iteration on the same RMax and RRMax:
[-maxIter3[ation] MaxIter3 (1 ).as(Integer ) ] :Optional :max iteration on the same RMax, RRMax, and Weight:
[-lambda lambda (1.0 ).as(Real ) ] :Optional :labda:
[-ctf CTF (0 ).as(Integer ) ] :Optional :CTF Compensation
[-WhiteNoise WhiteNoise (0.0 ).as(Real ) ] :Optional :White Noise
[-below below (90.0 ).as(Real ) ] :Optional :below
[-noantipole ] :Optional :No Antipole
[-magLimit ] :Optional :magLimit
[-eachTime ] :Optional :each time
[-continue Continue (NULL ).as(inFile ) ] :Optional :continue
[-forContinue ForContinue (NULL ).as(outFile ) ] :Optional :For continue
[-phi phimin (0.0 ).as(Real )
phimax (360.0 ).as(Real )
delphi (10.0 ).as(Real ) ] :Optional :phi:[degree]
[-z zmin (0.0 ).as(Real )
zmax (30.0 ).as(Real )
delz (5.0 ).as(Real ) ] :Optional :z:[A]
[-shift shiftmin (-10.0 ).as(Real )
shiftmax (10.0 ).as(Real )
delshift (1.0 ).as(Real ) ] :Optional :shift:[A]
[-log Log (stdout ).as(outFile ) ] :Optional :LogFile
[-Normalization ] :Optional :Normalization
[-pvm pvm (0 ).as(Integer ) ] :Optional :pvmNumber
[-pvmList pvmList (NULL ).as(inFile ) ] :Optional :pvmList
[-pvmServer ] :Optional :Work as a server !!
[-pvmClient ] :Optional :Work as a client !!
[-wd WorkingDir (./ ).as(String ) ] :Optional :Working Directory !!
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
-m 0: The 1st version algorism(Sharing)
-m 1: The 2nd version algorism(Least Square)
>> -ctf option <<
----- Mode -----
0: |CTFi|/Sigma(SQR(CTFi))
1: CTFi /Sigma(SQR(CTFi))
>> If -ctf, the file list indicated by -i must include the below information
filename weight defocus[A] Cs[mm] AccV[kV] ratioOfAmpToPhase mode
>> llDataSepartionControlFile <<
llMax(different)
nl Z numberOfN n0 n1 n2...