Hi all,

I am trying to navigate phenix.refine to occupancy refine a partially occupied inhibitor vs. the waters that it displaces.

For instance I have molecule resseq 802 in chain A, and waters 1-6 in chain W that are overlapping.  When just refining occupancy of the molecule there are clear sites for the waters.   How can I refine both of them together so that I can get an occupancy of the molecule vs the group of waters (which should have nearly identical occupancies)?

Maybe, a bit more information on the differences in refinement strategy for the occupancy vs fix occupancy vs group occupancy would be more broadly helpful.

I tried to make them all a group, but that didn't work as the refinement pushed the waters out and reduced their occupancies to ~0 while leaving the small molecule occupancy about the same as without water.