Re: [phenixbb] alternate conformation clashes with its symmetry mate

On Fri, Apr 13, 2012 at 5:01 PM, Page, Rebecca 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. -Nat