
| <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.