[phenixbb] Bulk solvent scaling & unstructured protein
PAfonine at lbl.gov
Wed Mar 24 09:26:32 PDT 2010
> 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.
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