[phenixbb] handling of alternate conformations
Ralf W. Grosse-Kunstleve
rwgk at cci.lbl.gov
Tue Jul 24 12:17:19 PDT 2007
Sorry for the late reply. I was out of town for a week.
> My first question is whether NCS constraints are also applied to alternate
Should be, but is not heavily tested.
All NCS restraints are listed in the .geo file created by phenix.refine
(assuming write_geo_file=True, which is the default).
Look for the long lists following "NCS restraint group". Do your
alternative conformation atoms appear in these lists?
> My second question concerns the atom count of the conformers, where the
> parts with non-alternating conformations seem to be included as well.
Pavel's explanation from last week is correct. Internally a "conformer"
is always a complete chain. The bond, angle, dihedral, chirality,
and planarity restraints are determined independently for each
conformer. This generates duplicate restraints which are checked
for consistency and then reduced again.
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