Re-extracting particles in cryosaprc that were imported from relion - missing particle location

[mvorlaender]

Hi there,

I have an issue when trying to re-extract particles in cryosparc. Here is the workflow so far:

-Motion- and CTF-correction and particle picking in warp, followed by extraction in Relion (particles were binned)
-Import of the binned particles in cryospsarc
-Classification and several rounds of refinement in cryosparc
-Now I want to change the boxsize and pixel size of the classified particles by re-extracting them in cryosparc. For this I have imported the motion-corrected micrographs from warp and ctf-corrected in cryosparc. When I connect the refined particles and the micrographs, the “location” field is empty

I am also attaching a screenshot of the original particle import job

Is this fixable? What would be the best way to avoid this in the future?

Thanks a lot in advance,
Best,
Matthias

[wtempel]

Welcome to the forum @mvorlaender. Please can you also share the content (from the beginning) of the Overview tab of that original particle import job. There may be an indication about why the location info is missing.

[DanielAsarnow]

You need to have the micrographs imported in cryoSPARC and link them as an input for the particle import. You will see in the import job output if rlnCoordinateX, rlnCoordinateY, and rlnMicrographName are imported and matched up with the micrographs.

[mvorlaender]

Thanks for the answers! Here is import job overview. I see the warning that there aren’t any micrographs connected. Can this be done at a later stage with the classified particles?

Thanks a lot for the help!

[DanielAsarnow]

You can do it at import, or with the reassign particles to micrographs job.