[phenixbb] [Feature request] Exclude atoms outside user provided mask from refinement (in phenix.real_space_refine)

[Oliver Clarke]

Hi,

Often I would like to refine part of a model against a EM map generated by masked refinement. Such a map is typically better than the globally refined map in the region within the mask, and worse outside it. 

It would be useful to have the capacity to refine the same model first against the globally refined map, and then against the maps generated by masked refinement, but restricting refinement in the latter case to atoms/residues within the bounds of the mask. 

Is this something that could be maybe added in a future version of phenix.real_space_refine? This would mean allowing the user to provide a mask file, and setting an option to exclude all atoms/residues outside the mask boundaries from refinement.

Cheers
Oli