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:

...

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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Dear Ralf, Thank you very much for your reply. OK, I stop worrying about solvent mask handling. Maybe my diffraction data have many problems (anisotropy, packing disorder, etc.) rather than solvent mask... Thanks again for all, K. Yamashita 2010/12/8 Ralf W. Grosse-Kunstleve :

Hi Keitaro,

...

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?

No, we're not doing anything special. -- I think it would be quite tricky to do something that's theoretically better than what we have right now, and I wouldn't be surprised if it didn't make any significant difference for the end results, after all the work.

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