Hi Ulrich,
My first question is whether NCS constraints are also applied to alternate conformations.
1) phenix.refine does not have NCS constraints but it has only NCS restraints. 2) I presume it will use whatever you specify in your selections for NCS groups (Ralf -- could you confirm this please?). If you include atoms in alternative conformation -- they will be used in NCS restrains.
My second question concerns the atom count of the conformers, where the parts with non-alternating conformations seem to be included as well
If I correctly understand your question, this is how alternative conformations are handled. Internally, for each conformer phenix.refine generates a separate chain. For example, if an atom in chain has 2 alternative conformations, then phenix.refine will create three chains-duplicates each containing unique conformation (one for main conformation and two for two alternative ones); each such created chain is called conformer. Pavel.