doc/SmallTools/ctfDetermine.html

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   2 <HEAD>
   3 <TITLE>ctfDetermine</TITLE>
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   5 <BODY>
   6 <H1>ctfDetermine</H1>
   7 <H2>Usage</H2>
   8 <PRE>
   9 Usage: ctfDetermine
  10 Options:
  11     [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile:  mrcImage
  12     [-o[utput]           Out                 (NULL      ).as(appendFile          ) ] :Essential :OutputDataFile: Parameters
  13     [-D[efocus]          Defocus             (0.0       ).as(Real                ) ] :Optional  :InitialDefocus[A]
  14     [-Cs                 Cs                  (1.7       ).as(Real                ) ] :Optional  :InitialCs[mm]
  15     [-Cc                 Cc                  (1.2       ).as(Real                ) ] :Optional  :InitialCs[mm]
  16     [-dE                 dE                  (0.2       ).as(Real                ) ] :Optional  :InitialCs[mm]
  17     [-Ac[cerratedVoltage]Ac                  (200       ).as(Real                ) ] :Optional  :Ac[kV]
  18     [-CutLow             CutLow              (0.05      ).as(Real                ) ] :Optional  :CutOffLowFrequncy[/A]
  19     [-CutHigh            CutHigh             (0.5       ).as(Real                ) ] :Optional  :CutOffHighFrequncy[/A]
  20     [-I0                 I0                  (1.0       ).as(Real                ) ] :Optional  :I0
  21     [-ratio              ratioOfAmpToPhase   (0.1       ).as(Real                ) ] :Optional  :ratioOfAmpToPhase
  22     [-Ai                 Ai                  (0.03      ).as(Real                ) ] :Optional  :IlluminationAngle[mrad]
  23     [-BofMTF             BofMTF              (15.0      ).as(Real                ) ] :Optional  :B of MTF [A]
  24     [-BofV[ibration]     BofVibration        (3.0       ).as(Real                ) ] :Optional  :B of Vibration [A]
  25     [-Mag[nification]    Magnification       (1.0       ).as(Real                ) ] :Optional  :Magnification
  26     [-[White]Noise       WhiteNoise          (0.0       ).as(Real                ) ] :Optional  :Signal/Noise Ratio
  27     [-[White]Noise2      WhiteNoise2         (0.0       ).as(Real                ) ] :Optional  :Signal/Noise Ratio
  28     [-MolcEnv            MolcEnv             (0.0       ).as(Real                ) ] :Optional  :Gaussian: Molcular Envelop [A]
  29     [-MolcEnv2           MolcEnvTable        (NULL      ).as(inFile              ) ] :Optional  :Table: Molcular Envelop
  30     [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
  31     [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
  32     [-min                min                 (-10       ).as(Real                ) ] :Optional  :min of coefficient area
  33     [-max                max                 (10        ).as(Real                ) ] :Optional  :max of coefficient area
  34     [-s[tep]             step                (0.01      ).as(Real                ) ] :Optional  :step of coefficient
  35     [-d[egree]           degree              (6         ).as(Integer             ) ] :Optional  :agree of function
  36     [-S[ection]          section             (4         ).as(Integer             ) ] :Optional  :section number of fft
  37 >>> Mode <<<
  38           0 : MinMax Methods (Henderson-like CTF determination)
  39           16: Fitting Methods
  40           32: Differential Methods
  41           64: Covariance Methods
  42           96: Differential & covariance  Methods
  43          128: MinSquare Methods
  44          160: Differential+MinSquare Methods by Imamura
  45          161: Differential+MinSquare Methods+NoiseRemoval(+1)
  46          163: Differential+MinSquare Methods+NoiseRemoval(+1)+EnvelopeFromLocalMaxima(+2)
  47
  48 </PRE>
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