I’m trying to do partial reconstruction for some phage-related data. When I do homologous refinement or helical refienment, the FSC curves have periodic huge dips or oscillation whether I apply symmetry or not (C1). I also tried to apply global CTF refinement on-the-fly but it helped litttle. Could some of you give me some suggestions?
Looks like a lot of beam tilt (or your pixel size is a long way off, can have the same effect). If global CTF refinement doesn’t make any difference, check the quality of the CTF fits closely.
Is your sample the size you expect (from output reconstructions)?
What did you enable (or disable) in global CTF refinement?
edit: Another thing that can cause this is if all micrographs/particles are the same defocus (because you get dips to zero in the CTF). However, the only time I’ve seen this actually caused this way is with simulated data.
I think the reconstruct map size is correct and pixel size doesn’t have big problem. I did on-the-fly global CTF refinement with default parameter. The defocus range is also shown below. How can I check the quality of CTF fit? Thanks~
Yes, defocus has a nice spread so it’s not that.
CTF fit can be checked in Manually Curate Exposures. A quick eyeball over the power spectra and simulated fits will be enough to tell you whether that is an issue.
Oh, I found I set wrong spherical aberration. The curve become normal after redoing CTF estimation. Thank you for your help!