mrcImageCTFDetermination
Usage
Usage: mrcImageCTFDetermination
Options:
[-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
[-r[eference] Ref (NULL ).as(inFile ) ] :Essential :ReferenceDataFile
[-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output Optimum [text]
[-oP[utput] Out2 (NULL ).as(outFile ) ] :Optional :Output Distribution [mrc image]
[-oC[utput] OutC (NULL ).as(outFile ) ] :Optional :Output CTF Information file
[-oF[utput] OutF (NULL ).as(outFile ) ] :Optional :Output Result FFT[mrc image]
[-kV kV (200 ).as(Real ) ] :Optional :AccVol[kV]
[-Cs Cs (2.1 ).as(Real ) ] :Optional :Cs[mm]
[-Ain Ain (0.02 ).as(Real ) ] :Optional :IlluminationAperture[mrad]
[-W[hiteNoise] WhiteNoise (1.0 ).as(Real ) ] :Optional :
[-df mindf (0.0 ).as(Real )
maxdf (200000 ).as(Real )
deldf (1000 ).as(Real ) ] :Optional :df[A] for in
[-AoverP minAoverP (0.0 ).as(Real )
maxAoverP (1.0 ).as(Real )
delAoverP (0.01 ).as(Real ) ] :Optional :AoverP[A] for in
[-Rmin Rmin (0.0 ).as(Real ) ] :Optional :Rmin[/A]
[-Rmax Rmax (0.1 ).as(Real ) ] :Optional :Rmax[/A]
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode]F[ilter type]mF (1 ).as(Integer ) ] :Optional :Filter Type
[-m[ode]W[ight type] mW (0 ).as(Integer ) ] :Optional :Wight Type
[-m[ode]S[um type] mS (0 ).as(Integer ) ] :Optional :Sum Type
[-m[ode]C[TF Info type]mC (0 ).as(Integer ) ] :Optional :CTF Information Type
[-M[ode] M (0 ).as(Integer ) ] :Optional :ref Type
[-PixelSize PixelSize (5 ).as(Integer ) ] :Optional :Pixel Size [A]
[-Width Width (120 ).as(Integer ) ] :Optional :Pad Width [pixel]
[-truePitch truePitch (430 ).as(Real ) ] :Optional :True Pitch [A]
[-dfRef firstDf (70000 ).as(Real )
withinDf (1000 ).as(Real ) ] :Optional :dfRef for ref
[-AoverPRef firstAoverP (0.05 ).as(Real )
withinAoverP (0.01 ).as(Real ) ] :Optional :A over P Ref for ref
[-MaxIter maxiter (10 ).as(Integer ) ] :Optional :MaxIteration for ref
[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
----- mrcFile -----
in <- Original Image
ref <- CTF Compensated Image
----- in <- Fiter Type (-mF) -----
0: No CTF compensation
1: Phase only: W = CTF/|CTF|
2: Multiply : W = CTF
3: Multiply : W = 1/CTF
4: Wiener filter (constant noise): W = CTF/(|CTF|^2+N^2)
5: Multiply : W = CTF^2
----- in <- Wight Type (-mW) -----
0: Weight = 1
1: Weight = (|in| + |ref|)/2
----- in <- Sum Type (-mS) -----
0: Sigma[Phase(i)]
1: Sigma[Phase(i)*Weight(i)] / Sigma[Weight(i)]
----- ref <- Type (-M) -----
0: CTF compensated single image
1: Three-dimentional reconstruction images that were made by
nea and far Bessel separation.
CTF compensatation were done between min defocus to max defocus.
This mode is for myosin filaments.
(Options) -PixelSize -Width -truePitch
-dfRef -AoverPRef -MaxIter
2: Result FFT
(Options) -oF, -dfRef, -AoverPRef
----- OutPut File-----
-o : defocus and amlitude-contrast at minimum point
-oP: mrc file
-oC: ctf information file for ctf compensation
Type (-mC)
0: lllExtractCtfinfFileCreate (mode 0)
1: lllExtractCtfinfFileCreate (mode 1)