[phenixbb] Dual conformation on symmetry axis
pafonine at lbl.gov
Thu Feb 4 13:49:30 PST 2016
> An Arg side chain is located very close to a crystallographic 2-fold.
> There is good evidence that the side chain has two conformations.
> However, because of the 2-fold, conformer A overlaps with its symmetry
> mate A*, as does conformer B. Phenix wants to avoid this 'clash' and
> moves A and A* out of the density, same for B and B*.
> Is there a way to avoid this without reducing the symmetry? In the
> real crystal, of course the two side chains are agnostic as to if they
> are called A or B and will avoid one another ...
you can exclude involved residue from repulsion by using this parameter:
custom_nonbonded_symmetry_exclusions="chain A and resseq 123 and (altloc
A or altloc B)"
You can do this in the GUI too by using search parameters option.
Let me know if it doesn't do it and I will think of an alternative solution.
More information about the phenixbb