Hi Matt, you will have to define the appropriate occupancy groups. I usually put that into a separate file (e.g. occ.params) which you then include as input. In your case this should do the job (I think ;-)): refinement { refine { occupancies { constrained_group { selection = (chain A and resseq 802) selection = (chain W and resseq 1:6) } } } } This should refine both selections to a sum of 1. More examples are at https://phenix-online.org/documentation/reference/refinement.html#occupancy-... Cheers, Eckhard Am 14.03.24 um 22:27 schrieb Matt Jordan McLeod:
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.
**Waters are only placed, they are not refined), small molecule is refined to 0.71 occupancy.**
-- *Matthew Jordan McLeod, PhD* Post-Doctoral Fellow |//Thorne Lab Cornell University G11 Physical Sciences Building 142 Sciences Drive Ithaca, NY 14853-3501 (607) 279 9382
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Prof. Dr. Eckhard Hofmann