<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 |
applyctf proj.hed proj.ctf.hed parmimg=start.hed applyctf
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.