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

Nicholas Sauter nksauter at lbl.gov
Tue Dec 7 09:00:15 PST 2010


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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