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