The center of map

Hi, how can I keep the center of a map which is C1 symmetry in homogenous refinement or other refinement? I find cryosparc use its own defined center for a map. Can I recenter my map and use it as a reference for refinement and keep the center of the output volume as my input volume? Thank you!


Hi @jianhaoc,

As far as I know, with C1 refinement, there isn’t any explicit re-centering of the volume done during homogeneous refinement. That being said, during the alignment search, we only search over shifts that are less than 20-30 % of the particle box size in magnitude, so the volume cannot be too far off center relative to the particle picks, or else particles won’t align properly. Are you noticing that with a C1 refinement, the volume moves between iterations, and if so, would you be able to show screenshots of the slice plots before and after?

Note that if you want to manually shift the volume/particles to a new center, we don’t have a utility to do this within cryoSPARC (but it is planned). I believe you would be able to do this using the move and vop resample commands in UCSF Chimera.