Is particle precentering neccesary or desirable for cryoSPARC refinement? Or is it robust to particle displacements within the box, assuming they are pretty much evenly distributed?
Overall strict precentering isn’t required, however if parameters are extremely off center you may need to turn windowing off which could lead to other problems, particularly if you have crowded images.
The particular case I was thinking about involved subparticles created using relion with signal subtraction, which consist of the peripheral domain of a larger particle - so they are quite a ways from the center of the box. However, so far at least cryoSPARC seems to be dealing with the situation okay in both classification and refinement. Thanks!
Oli