I fear that this may be a bit of a niche request, but would be really useful if possible to include.
In relion, it is possible to use a secondary solvent mask (–solvent_mask2) in 3d classification and refinement, for instance, that tells relion to ‘ignore’ the internal genomic density which is disordered thereby helping with alignment. I was wondering whether it would be possible to implement similar such mask out option for refinements in cryosparc? I appreciate that you offer ways around this (subtracting density etc.), but would be massively appreciated if this mask out option could be an option (if not already).