Hi Dan,
I am trying an identical pipeline as Sadeem for the first time.
From a homogeneous refinement job in cryoSPARC V2.5.0, I used the following:
csparc2star.py cryosparc_P#_JXX_particles.cs cryosparc_aligned.star (no --passthrough was required)
I also downloaded the map (both volume_map_halfA.mrc as well as volume_map.mrc from the same job.
To run 3D refinement in Relion, do I need match the boxsize with particle size?
Given the box size during extraction in local motion correction job was 360. The refinement box size during the prior hetero-refinement was 128 voxels, and the box size in the homogeneous refinement was set to NONE, which I think takes the value of 360.
Also which of the two maps should be used as a reference in Relion refinement?
If adjusting the boxsize in csparc2star.py required, my current pyem module gives the error:
csparc2star.py: error: unrecognized arguments: --boxsize 250
I do have the latest version (0.4).
Best,
Zuhaib