I found that the mask(the output of Nonuniform refinement）called cryosparc_volume_mask_fsc_auto.mrc only included the protein parts in my memprane protein. I was wondering whether I could use this type of mask for the following 3DVA protocol. Any bad influences?
If the mask looks sane and covers the parts you’re interested in, it will be fine. IIRC that mask can have some values close to, but less than, 1 inside the mask, so you might want to check that and possibly re-threshold it.