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====== applyctf ======
 //Applies/corrects CTF to sets of particle images//

===== Usage =====
 applyctf <input file> <output file> [setparm] [fixnoise] [parmimg=<input>] [memfile=<name>] [parmmem=<name>] [parm=<parmlist>] [sffile=<file>] [applyctf] [flipphase] [invert] [applyB[=<B factor>]] [addnoise[=<scale>]] [wiener] [mrc] [inplace]

==== Parameters ====
|| <input file>||Source file||
|| <output file>||Destination file, output overwrites existing images||
||[setparm]||Includes the CTF parameters in the header in the output images||
||[fixnoise]||n4 -> 0||
||[parmimg=<input>]||Extract CTF parameters from the first image in <input>||
||[memfile=<name>]||The file containing the CTF parameters, specify before "parmmem" option. default to ctfparm.txt in current directory, ||
||[parmmem=<name>]||Extract CTF parameters from ctfparm.txt with label <name>||
||[parm=<parmlist>]||Specify comma separated CTF parameters as specified in ctfparm.txt||
||[sffile=<file>]||File containing the structure factor associated with the fit parameters. Overrides value already specified.||
||[applyctf]||Applies absolute value of CTF as filter||
||[flipphase]||Flips phases||
||[invert]||Inverts the densities (ie - mult by -1)||
||[applyB[=<B factor>]]||Applies envelope function, optionally specify override for B factor||
||[addnoise[=<scale>]]||Adds defined noise level to image. Optional <scale> scales overall noise amplitude.||
||[wiener]||Apply a Wiener filter||
||[mrc]||Output image(s) in MRC format||
||[inplace]||Ouput image numbers same as input numbers, otherwise appends||
 Typical usage: applyctf proj.hed proj.ctf.hed parmimg=start.hed applyctf

===== Description =====
This program is used to apply or partially correct for the CTF in a set of particle images. Parameters may come from several sources, and each part of the correction may be individually enabled.

To fairly realistically simulate a micrograph use 'applyctf flipphase addnoise'. This assumes that the images are already filtered to an appropriate resolution. Note that the scale of added noise may be off and need adjustment.

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EMAN Manual page, generated Mon Jan  8 17:35:59 2007