Internal data binning for ab-initio/refinement


Working on reconstructing a virus with a box size of 1000. Ab-initio (no symmetry, single classs) generates a great initial model, but it takes a considerable amount of time to finish (~8 hrs - too long for cryoSPARC!). It would be great if one could bin their data by 2 or 4 for from inside the cryoSPARC to generate an initial model and then use unbinned for refinement.


Hi Mike,

I’m just a user so take this with a grain of salt, but I’m pretty sure cryoSPARC does that internally, controlled by the “Max resolution to consider” parameter in the setup.

You can check that by checking the box size of the resulting classes.

If you want it to go faster, and you just want an initial model that is good enough for refinement, maybe you could limit the max res to 20 Å or so (I think 12 is the default)?


Hi Oliver,
Your suggestion worked - it shortened the time it takes to run significantly. After carefully looking I also found the parameter “Refinement box size (Voxels)” which should take care of binning for refinement.