I have a refinement of a membrane protein in a nanodisc where I would like to supply a user-defined mask to mask out the nanodisc, as I suspect it is affecting my resolution due to jiggling of the protein in the nanodisc.
When I provide a user-defined, static mask, Cryosparc always uses it from the very first iteration, and the resulting refinement has quite substantial artefacts from masking, even though I have left a generous border around the protein when making the mask.
I suspect this is because cryosparc is applying the mask too early. When using dynamic masking, the dynamic mask only kicks in by default at 12 Å, but there is no similar option for static masks. Would it be possible to add such an option?