[phenixbb] No clash evaluation between symmetry mates in phenix.refine
yamashita at castor.sci.hokudai.ac.jp
Tue Dec 7 17:40:47 PST 2010
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,
2010/12/8 Nicholas Sauter <nksauter at lbl.gov>:
> 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
> <yamashita at castor.sci.hokudai.ac.jp> 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
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