I have run in a roadblock in switching cryosparc and relion for the purpose of performing different processing steps on the same dataset. In particular, I am struggling to produce the correct star files as inputs for Bayesian Polishing. Please see my case below; I would really appreciate if anyone has suggestions about good workflows or scripts to make the transition workable.
I import, patch motion correction, patch ctf estimation, particle picking and extraction, 2D classification, ab initio reconstruction and homogenous refinement in cryosparc. I find it to be a fast and robust way of getting an first pass reconstruction and good particle set.
Then, I use cspar2star.py (thanks @DanielAsarnow !) to export the stack from the .csv produced from the refinement and, with minor adjustments, import the particles into relion to harness the power of its 3D classifier, 3D auto-refine, beam tilt correction / ctf-refine.
Now, I would like to perform Bayesian Polishing, which requires (nominally, please correct me if I am wrong):
(1) a micrograph star file that points to motion-corrected mrc files with associated metadata files (is it possible to generate these for the cryosparc patch motion correction outputs?)
(2) a particle star file (e.g. from CtfRefine or 3DRefine)
(3) a PostProcess star file
Is it possible to use the cryosparc motion corrected micrographs in any way? Or is it easier to re-run the motion correction through the relion GUI, and then edit star files to point to the relion MotionCorr outputs rather than to the cryosparc ones? If so, will particle coordinates be compatible between the two outputs?
Thank you for reading and thank you for all past/future advice!