mrcImageCTFDetermination

Usage

Usage: mrcImageCTFDetermination
Options:
    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
    [-r[eference]        Ref                 (NULL      )] :Essential :ReferenceDataFile
    [-o[utput]           Out                 (stdout    )] :Optional  :Output Optimum [text]
    [-oP[utput]          Out2                (NULL      )] :Optional  :Output Distribution [mrc image]
    [-oC[utput]          OutC                (NULL      )] :Optional  :Output CTF Information file
    [-oF[utput]          OutF                (NULL      )] :Optional  :Output Result FFT[mrc image]
    [-kV                 kV                  (200       )] :Optional  :AccVol[kV]
    [-Cs                 Cs                  (2.1       )] :Optional  :Cs[mm]
    [-Ain                Ain                 (0.02      )] :Optional  :IlluminationAperture[mrad]
    [-W[hiteNoise]       WhiteNoise          (1.0       )] :Optional  :
    [-df                 mindf               (0.0       )maxdf               (200000    )deldf               (1000      )] :Optional  :df[A] for in
    [-AoverP             minAoverP           (0.0       )maxAoverP           (1.0       )delAoverP           (0.01      )] :Optional  :AoverP[A] for in
    [-Rmin               Rmin                (0.0       )] :Optional  :Rmin[/A]
    [-Rmax               Rmax                (0.1       )] :Optional  :Rmax[/A]
    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
    [-m[ode]F[ilter type]mF                  (1         )] :Optional  :Filter Type
    [-m[ode]W[ight type] mW                  (0         )] :Optional  :Wight Type
    [-m[ode]S[um type]   mS                  (0         )] :Optional  :Sum Type
    [-m[ode]C[TF Info type]mC                  (0         )] :Optional  :CTF Information Type
    [-M[ode]             M                   (0         )] :Optional  :ref Type
    [-PixelSize          PixelSize           (5         )] :Optional  :Pixel Size [A]
    [-Width              Width               (120       )] :Optional  :Pad Width [pixel]
    [-truePitch          truePitch           (430       )] :Optional  :True Pitch [A]
    [-dfRef              firstDf             (70000     )withinDf            (1000      )] :Optional  :dfRef for ref
    [-AoverPRef          firstAoverP         (0.05      )withinAoverP        (0.01      )] :Optional  :A over P Ref for ref
    [-MaxIter            maxiter             (10        )] :Optional  :MaxIteration for ref
    [-m[ode]             mode                (0         )] :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)