Cryosparc2star.py for subtracted particles

Import and Export
1

Hi @DanielAsarnow

I would like to perform focused 3D classification w/o alignment in Relion using signal-subtracted particles with a reference volume and mask from local refinement in cryosparc.

I have converted my exported .cs file containing these particles to .star but just want to check, should I skip sed -i 's/particles.mrc/particles.mrcs/g' from_csparc_P7J369.star (which is normally done for a particle.star file that points to extracted particles but my .star doesn’t contain .mrc) and create symlinks to the .mrcs files contained in the signal subtraction job?

Here is a line from my star file:

000384@J343/subtracted_particles_batch_110B.mrcs J10/imported/FoilHole_9138183_Data_7120097_7120099_20191009_1927_fractions.mrc 345 1802 107.785454 64.232979 56.879372 0.378805 1.374681 13332.370117 13311.297852 -22.611738 0.000000 0.000000 4 2 1

2

The only purpose for the .mrcs renaming is that Relion will refuse to read particles from stacks with a .mrc extension, so if I get you right what you have will work.

You might also want to have a Relion project directory that’s outside the cryoSPARC project tree, in which case you could make a link there directly to the J343 directory.

3

Thanks @DanielAsarnow that worked well :slight_smile: