Re: [phenixbb] No clash evaluation between symmetry mates in phenix.refine

Dear Nicholas, Thank you very much!! That is what exaclty I need and it works fine. By the way, in this situation, I'm wondering what the appropriate way for bulk solvent correction is. How is the solvent mask calculated in phenix.refine? Is the protein region, which overlaps with symmetry mates, included in solvent mask with smaller occupancies? Thank you again for everything, K. Yamashita 2010/12/8 Nicholas Sauter :

Keitaro,

The pdb_interpretation.custom_nonbonded_symmetry_exclusion=<selection> command line keyword was designed for this purpose.  It is also available from the GUI by searching under all parameters.

Nick Sauter

On Tue, Dec 7, 2010 at 4:36 AM, Keitaro Yamashita wrote:

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Dear Phenix developers,

I have a question about phenix.refine.

I'm refining complex structure against X-ray diffraction data with packing disorder. (Some domains overlap with their symmetry mates (4-fold), so their occupancies are set to 0.25)

So I want phenix.refine to ignore clashes between symmetry mates. Can phenix.refine exclude any interaction between symmetry mates from geometric term in target function: E = E(x-ray) + E(geometry)? Is there any option?

Thank you very much in advance,

K. Yamashita _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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