[phenixbb] handling of alternate conformations

[Ralf W. Grosse-Kunstleve]

Hi Ulrich,

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
> conformations.

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.

Ralf