[phenixbb] Bulk solvent scaling & unstructured protein

Pavel Afonine PAfonine at lbl.gov
Wed Mar 24 09:26:32 PDT 2010

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.


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