How would I go about running CtfRefine in Relion3.1 after CryosparcV2 homogenous refinement? I need a particles star file and a postprocess star file to run . I used pyem command below to get a particles star file. Could I use the half maps from cryosparc job and the converted particles.star file to get a postprocess.star file directly?
mentioned _rlnRandomSubset being random and not saved in cryosparc . So I would have to refine again in relion or run local refinement in cryosparc? And that halfmap could be used in relion postprocess. If I am using the same mask from the homogenous run would I need to extract any differently?
The half map split is saved by cryoSPARC after a refinement, and rlnRandomSubset should be populated when you convert back to a .star file. The other thread is talking about what happens when you import particle alignments or re-run new refinements in cryoSPARC.
How would you suggest extracting and preparing my particles.star and postprocess.star after cryosparc when my end goal is to merge datasets and run CtfRefine?
I get a very noisy map after pp if I use the half map in relion to get a postprocess.star file.
Is the postprocess map you showed masked or unmasked? It’s normal for unmasked sharpened maps to have a lot of dust, since you’ve just boosted the high-frequency components a lot. You might want to try some manual b-factor selection, like -80, -100 instead of the automatic one which might be a lot higher.
You can also see if it works better with relion_reconstruct --subset 1 to do two half-map reconstructions instead of the ones from cryoSPARC. Another option is to do one iteration (or just let it converge) of local angle search in Relion.