Going from cryosparc to relion back to cryosparc

Import and Export
1

Hi all,

I started my processing in cryosparc and got to a refined model before importing into relion with csparc2star. After 3D classification in relion i’ve done symmetry expansion on my particle stack and want to then take this star file and extract these local coordinates in cryosparc with a smaller box size. If I just put the star file into the import particles job under the particle meta path tab i get an error after about an hour (slurmstepd: error: Detected 1 oom-kill event(s) in StepId=40472993.batch. Some of your processes may have been killed by the cgroup out-of-memory handler.). I increased the memory allocated to 100Gb over the star file and it still spits out this error. Any insight? If i have not given enough info please just ask I’m somewhat new to this.

Best,

Tyler

2

@tbrittai How many particles are you trying to import?

4

@wtempel after symmetry expansion ~6.6 million.

5

We wonder whether the OOM is caused by the large number of particles, or by something else.
What happens if you continue to allocate are large amount of RAM, but import particles based on a smaller star file, perhaps corresponding to the non-symmetry-expanded particle set?