Ctf_create_ctfdat

ctf_create_ctfdat

Purpose

This utility allows you to create CTFdat files from a selfile that contains image selfiles for each micrographs. To provide the CTF information, there are two modes. In mode 1 one provides a single CTFparam file with the common characteristics of all micrographs (see example below) and a docfile with the defocus values for each micrograph. In mode 2 one provides a selfile of CTFparam files for each micrograph. Note that the number of entries and the order of the selfile of CTFparam files and the Docfile with defocus values should correspond to the number of entries and the order in the input selfile of selfiles.

Usage

$ ctf_create_ctfdat

Parameters

• `` The input selfile, containing the image selfiles for each micrograph.
• -o [rootname"out"] = Rootname for output files..ctfdat will be added to the CTFdat file, and in option 1, CTFparam files will be written for each micrograph with namerootname?????.ctfparam.

For mode 1:

• `` CTFparam file containing the common parameters (microscope kV, Q0, etc)
• `` docfile with defocus values for each micrograph. This docfile may contain a single column (defocus for non-aniostropic micrograph) or have three columns (defocusU, defocusV, azimuthal_angle). Note that the number of entries and the order should be the same as for the input selfile of selfiles.

For mode 2:

• • `` selfile with CTFparam files for each micrograph. Note that the number of entries and the order should be the same as for the input selfile of selfiles.

Examples and notes

Using mode 1

$ ctf_create_ctfdat -i my_micrograph_selfiles.sel -param common.ctfparam -doc my_micrograph_defocus.doc

Wherecommon.ctfparam could be:

sampling_rate=        2.82
voltage=              200
spherical_aberration= 2.0
Q0=                   -0.1

Andmy_micrograph_defocus.doc could be:

1 1 -11600.
2 1 -15900.
3 1 -17540.
4 1 -17450.

Using mode 2:

$ ctf_create_ctfdat -i my_micrograph_selfiles.sel -ctfs my_micrograph_ctfparams.sel

--Main.SjorsScheres - 09 Apr 2008