NoteOnCtfGroups

CTF groups

It is common practice to group images with similar CTF parameters into CTF groups. Note that inside the MLF programs CTFs are assumed to be non-astigmatic (i.e. defocusU=defocusV). All images in one group should have the same CTF parameter file in the second column of the CTFdat file. In general, we recommend at least 100-200 particles in each group, and it's usually a bad idea to go below 50 particles per group (as the estimation of the corresponding noise spectra may become unstable).

Standard Xmipp protocols for data preprocessing (see GettingStartedWithProtocols) provide CTF parameter files for each micrograph and the corresponding CTFdat file for the entire data set. But, the estimated CTFs for each micrograph are usually astigmatic and no grouping is performed. Generating CTF groups with only non-astigmatic CTFs and the corresponding CTFdat file for the entire data set is a tedious job. In the future we will try to provide a more automated way of making these groups inside the standard protocols. For the moment, the MakeCTFGroupCsh shell script may be of help. Save it asmake_ctf_groups.csh in your Preprocessing/ sub-directory, generate the requested selfiles of all CTF parameter files and all corresponding selfiles of windowed particles for each micrograph, and execute the first part of the script by typing:

./make_ctf_groups.csh 1

Then, decide on the division points (defocus values) for each group, edit the script header correspondingly, and execute the second part of the scripts by typing:

./make_ctf_groups.csh 2

This will automatically generate the needed CTFdat file needed to run the MLF programs.

If you come from outside the standard Xmipp protocols, note that the format of the non-astigmatic CTF parameter file needed by the MLF prgrams is as follows:

defocusU= -54000
defocusV= -54000
Q0=  -0.1
voltage=  200
spherical_aberration=  2.26
sampling_rate=  4.2
K= 1.0

WheredefocusU should be equal todefocusV and both are in Angstroems,Q0 is the amplitude contrast (should be negative!),voltage is in kV, andsampling_rate is the pixel size in Angstroms.

--Main.SjorsScheres - 28 Nov 2007