defocusDeterminationFromThonRing
Usage
Usage: defocusDeterminationFromThonRing
Options:
[-i[nput] In (stdin ).as(inFile ) ] :Optional :InputDataFile
[-i[nput] N[ame] InN (stdin ).as(String ) ] :Optional :InputNameInInformationFile
[-i[nput] R[eference]InR (stdin ).as(String ) ] :Optional :InputReferenceForLength
[-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
[-o[utput] I[nformation]OutI (stdout ).as(outFile ) ] :Optional :OutputInformationFile
[-o[utput] I[nformation]OutI2 (stdout ).as(outFile ) ] :Optional :OutputInformationFile
[-o[utput] I[nformation]OutI3 (stdout ).as(outFile ) ] :Optional :OutputInformationFile
[-kV kV (200 ).as(Real ) ] :Optional :kV
[-Cs Cs (2.1 ).as(Real ) ] :Optional :Cs[mm]
[-A[mplitude contrast]AoverP (0.05 ).as(Real ) ] :Optional :The ratio of amplitude contrast to phase contrast
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
[-ctfMode ctfMode (0 ).as(Integer ) ] :Optional :CTFMode
[-truePitch truePitch (430 ).as(Real ) ] :Optional :True Pitch
[-PixelSize PixelSize (5 ).as(Real ) ] :Optional :Pixel Size [A]
[-deltadY deltadY (0.5 ).as(Real ) ] :Optional :A range of deltadY to determine dY.
[-R[/A] R (NULL ).as(Real ) ... ] :Variable :ThonRing[/A]
----- Additional Usage -----
>>>> o[uput] I[nformation] <<<<
This file is used for [mrcImageMultiCTFCompensation and mrcImageCTFCompensation]
>>>> o[uput] I[nformation] 2<<<<
This file is used for [llDataCTFCompensate -I2]
>>>> o[uput] I[nformation] 3<<<<
This file is used for [llExtractWithLayerSeparation]
Options: -truePitch, -PixelSize, -deltadY and -ctfMode
>>>> ctfMode <<<<
0: Phase CTF
1: PhaseCTF + ratio*AmpCTF
>>>> mode <<<<
No action