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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.

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

EMAN1/Programs/ApplyCtf (last edited 2008-11-26 04:42:28 by localhost)