Is it possible to tell phenix.refine to ignore certain non-bonded interactions? I have a structure at 1.1A with some interesting sulfate molecules that refuse to refine well. I suspect two positions are alternately occupied by sulfate in some cases and two water molecules in others. I would like to refine with both (a sulfate and two waters) with each component at 1/2 occupancy. With alternate conformations of a given sidechain, the two alternate locations automatically ignore one another w.r.t. non-bonded interactions. However, different residues, it would seem, do not. Has anyone encountered a similar situation or do the phenix gurus have any input? As an alternative, can I define an alternate sulfate residue with several missing atoms? Thanks in advance, --Paul