Hello, I am trying to export a particle stack from cryosparc into relion so that I can perform Bayesian polishing in relion.
I used csparc2star to convert the particle stack from cryosparc to relion, then modified the path for the motioncorrected micrographs so that it points to the relion motion correction and not the cryosparc motion correction.
As a check, I attempted to re-extract the particles from the relion micrographs, and everything ran fine until the very end of the extraction, as shown in the output log:
=== RELION MPI setup ===
- Number of MPI processes = 4
- Leader (0) runs on host = cd-grout.mit.edu
- Follower 1 runs on host = cd-grout.mit.edu
- Follower 2 runs on host = cd-grout.mit.edu
- Follower 3 runs on host = cd-grout.mit.edu
- Re-extracting particles based on coordinates from input _data.star file
Extracting particles from the micrographs …
1.70/1.70 hrs …~~(,_,">
Joining metadata of all particles from 21653 micrographs in one STAR file…
RELION version: 4.0-beta-1
exiting with an error …
The error message was:
ERROR: optics group “” does not exist in micrograph STAR file…
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
I think this has to do with the fact that even though I changed the motion correction path to the relion micrographs, I haven’t changed the star file parameters associated with the relion-processed micrographs (i.e., the values for rlnOpticsGroupName, rlnCtfBfactor, rlnDefocusU, rlnDefocusV, etc.). Can anyone tell me how to update the star file from cryosparc with these values from the relion-processed mics?
Additionally, can anyone tell me if I’m amiss in my approach here? I’d like to take these particles and, in relion, do a quick round of 3D classification, then 3D auto-refine, then per-particle CTF estimation and Bayesian polishing, so I need to make sure that the star file generated from the cryosparc particle stack works with the relion-processed micrographs.