[phenixbb] Partial occupancy refinement of overlapping inhibitor+water sites

[Nigel Moriarty]

You can read more here.

https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : NWMoriarty at LBL.gov
Web  : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464


On Sun, Mar 17, 2024 at 3:53 PM Eckhard Hofmann <eckhard.hofmann at rub.de>
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-refinement
>
> 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 <eckhard.hofmann at rub.de>
> 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
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