You can read more here. https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN... Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : NWMoriarty@LBL.gov Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 On Sun, Mar 17, 2024 at 3:53 PM Eckhard Hofmann wrote:

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 Ruhr-Uni Bochum AG Proteinkristallographie ND04/318, Fachnummer 50 44780 Bochum Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762 ORCID: 0000-0003-4874-372X _______________________________________________ phenixbb mailing list phenixbb@phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave@phenix-online.org