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