Hi Laurie,
I notice that during refinement of a MR solution for a protein (search model is 100% homologous to target), a very large ligand-binding cavity (as much as 20 A wide in some parts) in my protein gives weak positive difference density for a ligand soaked into the crystals, unless I turn off bulk solvent modeling. Then the fo-fc difference density is quite strong (2.6 Angstrom data). I think this is due to part of the cavity being included in bulk solvent?
Can I edit the mask easily, or flag parts of the protein as NOT exposed to solvent?
no, right now there is no quick&easy way to do this. Several people reported the same observation in the past. So probably I will do something about it at some point. For now, I can suggest two options: 1) If you see the ligand now (when you turn off the bulk-solvent) then just build it, or 2) Fill the space where the ligand is supposed to be with dummy atoms (water for example) that all have zero occupancy. And when you run phenix.refine with those dummy atoms make sure you use "refinement.mask.ignore_zero_occupancy_atoms=False" keyword. Also, make sure you exclude the DA from coordinate and ADP refinement too. You can use phenix.grow_density to generate dummy atoms in spheres of defined radius placed in defined points. Let me know if you need any help with this. It would be helpful if you send me the data and model files, and indicate where the ligand is supposed to be. Then, once I get a chance to work on this problem (probably not very soon), it will be very useful to have a specific example. Pavel