I am trying to process some negative stain data and from what I have read CTF correction can be problematic for that. is it possible to skip that step?
I missed this, and so I am late replying - but for future sake - if you set the defocus values to 0, CTF will be skipped. The easiest way do to this is to change the defocus values for the images to 0 and re-extract the particles. The following commands would work :-
first backup your .db project file, and make sure the project is closed
sqlite3 you_database_name.db
update estimated_ctf_parameters set defocus1=0.0, defocus2=0.0;
.quit
Then reopen the project, remake your refinement package and any jobs run with that, will not use CTF.
I missed this, and so I am late replying - but for future sake - if you set the defocus values to 0, CTF will be skipped. The easiest way do to this is to change the defocus values for the images to 0 and re-extract the particles. The following commands would work :-
first backup your .db project file, and make sure the project is closed
sqlite3 you_database_name.db
update estimated_ctf_parameters set defocus1=0.0, defocus2=0.0;
.quit
Then reopen the project, remake your refinement package and any jobs run with that, will not use CTF.
Thanks
Tim