search

3dem / relion

Image-processing software for cryo-electron microscopy
https://relion.readthedocs.io/en/latest/
GNU General Public License v2.0
456 stars 203 forks source link

incorrect reporting of CTFFIND4 vs CTFFIND3 #1183

Closed huwjenkins closed 2 months ago

huwjenkins commented 2 months ago

When RELION-5 (5.0-beta-3-commit-12cf15) runs CTFFIND4 even if the --is_ctffind4 flag is given (which is added by default by the GUI) the logfile contains:

Estimating CTF parameters using Niko Grigorieff's CTFFIND ...

Which should not be the case:

https://github.com/3dem/relion/blob/12cf15de1ae8c30aed8da98cc2889a965e8b8814/src/ctffind_runner.cpp#L361-L364

This suggests is_ctffind4 is not being set correctly. This may just be a reporting issue - job seems to run fine.

biochem-fan commented 2 months ago

Interesting. We can investigate it but perhaps we should completely drop CTFFIND3 support at the same time.

@scheres, what do you think?

huwjenkins commented 2 months ago

Actually I think this line is actually written to the logfile from here:

https://github.com/3dem/relion/blob/12cf15de1ae8c30aed8da98cc2889a965e8b8814/src/ctffind_runner_mpi.cpp#L51

Sorry for the confusion - but dropping CTFFIND3 support would clean up the code a bit.

huwjenkins commented 2 months ago

Confirmed relion_run_ctffind (i.e. without MPI) correctly prints:

Estimating CTF parameters using Alexis Rohou's and Niko Grigorieff's CTFFIND4.1 ...