Relion_reconstruct failed after re-extract refined particles from cryosparc

[uhnsoo]

Hello,

We try to extract particles in relion (v. 4.0) using home-refined particles from cryosparc (v.4.4.1) and attempted to generate the same 3D map using relion_reconstruct.

. pyem (version 0.5)

. csparc2star.py xxx_particles.cs xx_passthrough_particles.cs xxxx.star

. using vi commend, change ‘_rlnMicrographName’ to micrograph names in MotionCorr/jobxx/Micrographs/xxxx.tif

. extract particles with an option of re-extract refined particles

. relion_reconstruct --i Extract/jobxx/particles.star --o Extract/jobxx/map.mrc --ctf --angpix xx

particle extraction seems to work (based on 2D classification), but relion_reconstruct failed to generate the same 3D map derived from cryosparc homo-refine.

it seems like ‘_rlnAngleRot’, ‘_rlnAngleTilt’, ‘_rlnAnglePsi’ info were transferred to .star file.

Does anyone know what the problem is?

Uhnsoo

[cryofun]

How different is your relion refined map from the cryosparc refined map?

If you import those particles to cryosparc and refine against that cryosparc map, do you reach the same result?

I have a similar issue

Cannot replicate refinement from cryosparc after csparc2star

I am encountering a strange issue after running csparc2star. My goal is to extract particles without normalization after running standard processing in cryosparc. Since cryosparc cannot do this, I must extract in relion. I am not extracting without normalization, yet, just testing the pipeline with normal settings that should be consistent with cryosparc processing. My current issue is that when I run csparc2star.py, extract particles in relion, then import those particles to cryosparc and run …

[cryofun]

If you are re-extracting in relion from the same set of micrographs as extracted from in cryosparc, I believe you need to use the flag --flipy in csparc2star.py.