Instructions for Performing Relion Polishing Using Refinement Folders from CryoSPARC

[unaginekomoyashi]

"Please teach me how to specify the folder for refinement in cryosparc and perform polishing with relion using cs2star."

[brisvag]

Hi @unaginekomoyashi! Refinement jobsa should work the same as everything else. Assuming the path to your cryosparc project folder is /path/to/project/, the job number is 123 and that you want the output in the current working directory, you should be able to simply use:

cs2star -pm /path/to/project/J123

[unaginekomoyashi]

Thank you for your comment. When attempting to perform polilsh using relion with the micrographs.star and particles.star files, I encountered the following error:

ERROR:
The corrected_micrographs STAR file does not contain rlnMicrographMetadata label. Did you not run motion correction from the RELION-3.0 GUI?
I would appreciate any comments or suggestions on how to resolve this issue.

[brisvag]

Ah I see; you're trying to run bayesian polishing in Relion? This won't work. As stated by the error, the micrographs must undergo motion correction in relion in order for it to know how to do polishin. This means that you can't polish particles that come from micrographs motioncorrected in cryosparc, unfortunately.

You can still do this if you want, but first you need to:

• re-run motioncorr from relion and get new micrographs
• edit the micrograph paths in the starfile from cs2star so they point to the new micrographs
• re-extract the particles from relion from the new micrographs
• do polishing

It's a bit trickier and you'll have to do some scripting, but it can work.