When I run the new homogeneous refinement, the defocus and ctf refinement is automatically off in input tab when I check it after job starts.
I did not find there is a switch when I build the job. Anyone knows how to turn them on?
They should be there in the builder, whether or not you have advanced params exposed, so not sure what is going on in your case - this is what it looks like for my system:
Thank you olibclarke. After I turn on “New job”, the switch appears.
Ah - that is the switch for advanced parameters. In my case if I switch it off, the defocus and global ctf refinement options remain, but glad it is working for you now!