Re-extract particle from downscale micrograph

Particle Picking
1

Hi there,

For the same dataset, I ran two Patch Motion jobs, separately, one came out with bin1 micrographs, and the other one came out with bin2 micrographs. For the bin2 micrographs, I’ve successfully extracted particles that can generate good 3D volume. Now, I want to re-extract the particles from the bin1 micrographs. If you have any ideas?

2

Reassign the particles to the bin1 mics (using “Reassign particles to micrographs”), then extract.

3

Hi Olibclarke, thank you for the info. I tried the job, but somehow, cannot find the micrographs, if you have any guess? here is error message
Traceback (most recent call last): File "cryosparc_master/cryosparc_compute/run.py", line 95, in cryosparc_compute.run.main File "/home/groups/brunger/software/cryosparc/cryosparc_worker/cryosparc_compute/jobs/utilities/run_reassign_particles_mics.py", line 70, in run_reassign_particles_mics assert qname in inv_index_source, "Could not find match for %s" % qname AssertionError: Could not find match for 20230625grid11_E4KO_ISV_188-131_00001_X-1Y-1-1_patch_aligned_doseweighted.mrc

4

Have you applied appropriate cuts to filename prefixes and suffixes (guide)?

5

Yes, I did multiple tries, but I found I don’t need to provide the cut number. Since my bin1 and bin2 micrographs are both done by CryoSparc, so the only difference is the UID number, which the job itself can recognize.