Hi Ed,
just to make sure you are looking at the updated manual:
http://www.phenix-online.org/documentation/refinement.htm#anch20
Yes, you are right, ideally one would constrain occupancy between Qmin
and Qmax. Answering your question: no, with the current version you
cannot constrain the sum of occupancies to <1 (or to Let's say there are two orientations of a ligand for which occupancies
need to be refined. By default, the sum of the two will be fixed at
1.0. From quick look at the manual, the only way to have the sum(occ)
at lower level is to reset main.occupancy_max. However, this will
probably affect all the atoms for which occupancies are refined, which
is undesirable (while ligand may have total occupancy of<1, alternate
conformers for protein residues should always add up to 1). Am I missing something or the only way to get this done is to refine
twice - once only for ligand occupancy, and then for the rest of the
model. And what if total occupancy of the ligand is unknown? Is there a way to
allow sum(occ) to be anywhere between 0 and 1?