[phenixbb] alternate conformation clashes with its symmetry mate

Nathaniel Echols nechols at lbl.gov
Fri Apr 13 17:48:26 PDT 2012

On Fri, Apr 13, 2012 at 5:01 PM, Page, Rebecca <rebecca_page at brown.edu> wrote:
> I have a protein in which the N-terminal residue is in two
> conformations.When the residue is in the 'A' conformation, the sidechain
> overlaps with the 'A' conformation sidechain density of its symmetry mate. I
> have modeled the occupancy at 50%. However, every time I refine, phenix
> pushes the 'A' conformer out of the density, likely due to clashing with its
> symmetry mate.
> Is there anyway to get around this?

I think this is what the parameter
"custom_nonbonded_symmetry_exclusions" is for - it specifies an atom
selection for which to turn off these interactions.


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