Symmetry expanded particles and cache

Troubleshooting
1

Dear cryoSPARC developers.

I would like to report what I experiences several times when using symmetry expanded particles, when they were expanded into cryoSPARC. This also happens to imported relion-expanded stacks if subsequent subtraction/downscaling/etc… is performed in cryoSPARC.

When loading particles to cache, cryoSPARC transfers particles corresponding to the first symmetry operand, but then load the particle stacks corresponding to all the other symmetry operation applied. The latest stacks being copies of the initial stack with different orientations. By doing so, cryoSPARC erases previously loaded particles if space on the scratch is not sufficient. This makes following jobs crashing since then some stacks are missing. This forced me to turn off caching and of course significantly slow down the jobs.

Would it be possible for cryoSPARC to load the particle stack only once, then apply the symmetry operations to this stack only during refinement ?

Hope you can solve this problem,

Nils

2

Hi @marechan,

Symmetry expansion in cryoSPARC does not actually duplicate any particle data, and the caching system also only caches the particles once rather than once per symmetry expansion. However, if you run signal subtraction or downsampling, new particle .mrc files are written for each input particle, including all symmetry expanded copies. These would then all get cached separatetly. Does this explain the phenomenon you’re seeing?

3

This actually explains it, thanks !

best regards,

Nils