Hi Michael @mmclean, can you please explain what the difference would be between a particle subtract mask created from 2 binarized masks (vop subtract #maskX #maskA), where both masks have been binarized prior to vop subtract, but not soft-padded v/s a particle subtract mask created from, say, 2 molmaps (vop subtract #molmapX #molmapA), where both molmaps are created at the same resolution of 12A, and then the resultant map is converted to a mask in cryosparc by applying a threshold for binarization and soft padding? Would the former strategy work better for creating masks for small subunits within a protein complex, since with already binarized masks, there won’t be a problem with ‘floating “specks” of density’ that can sometimes be an issue for smaller regions of interest?
Thanks for your help!