How to import micrographs.star files from Relion to cryoSPARC

Troubleshooting
1

Hi, I am trying to import same subset of micrographs in Cryosparc selected in relion while manual picking.or How to export micrographs.star files (generated after manually selecting micrographs subset in ManualPick) from Relion to Cryosparc? I actually want to use same set of micrographs in Cryosparc that I used in Relion and then continue with particle picking.
Thanks
Sangeeta

2

Hi @SangeetaNir,

CryoSPARC can import particle .star files but not micrograph .star files - in this case you would need to simply import the micrographs themselves (i.e. as a folder full of .mrc files) and then continue processing in cryoSPARC

3

Hi @apunjani,

I want to import motion corrected and CTF correctecd micrographs to CS to do the following process because our hardware can’t run patch motion correction in CS (always out of memory).

Followed your suggetions here, I imported the .mrc files generated from CTFFIND-4.1 in relion 3.1 sucessfully. I assumed these files were motion corrected and with CTF information. Then I tried to run ‘blob picker’ and got an error message:

[CPU: 90.5 MB] Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 52, in cryosparc2_compute.run.main
File “cryosparc2_compute/jobs/runcommon.py”, line 823, in check_default_inputs
assert False, 'Non-optional inputs from the following input groups and their slots are not connected: ’ + missing_inputs + ‘. Please connect all required inputs.’
AssertionError: Non-optional inputs from the following input groups and their slots are not connected: micrographs.ctf. Please connect all required inputs.

Then I though perhaps I could run the CTF estimation again in CS. And I did it and job finished, but the thon rings look quite odd. The CTF estimation using CTFFIND-4.1 was good for most of micrographs.

Can I ask your suggestions of how to import motion corrected with (or without) CTF estimated micrographs from Relion to CS? I would like to do these two steps in CS if possible, but our hardware is not good enough to run patch motion correction job in CS (K3 super-resolution data set). The patch has been installed, GPU has been reduced as suggested in other thread.

Thanks very mun!
Yahui