Re: [phenixbb] Bulk solvent scaling & unstructured protein

Hi Mads,

My question is now: Is there an approach to optimizing bulk solvent scaling in Phenix, keeping with the thought, that 30-35% of my protein sequence should be present where Phenix assigns bulk solvent.

yes, with some (slightly tedious) manual work -:) Fill the area where you expect the protein to be with dummy atoms (say water). Make sure that: 1) all DA have zero occupancy so they don't contribute to the scattering; 2) tell phenix.refine to include zero occupancy atoms into mask calculation: "refinement.mask.ignore_zero_occupancy_atoms=False", so the bulk solvent does not enter that area. Let me know if you have questions. Pavel.