<div dir="ltr">You can read more here.<div><br></div><div><a href="https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12">https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12</a></div><div><br></div><div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><font face="arial, sans-serif">Cheers</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Nigel</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">---</font></div><div><font face="arial, sans-serif">Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</font></div><div><font face="arial, sans-serif">Lawrence Berkeley National Laboratory</font><br><font face="arial, sans-serif">Berkeley, CA 94720-8235</font><br><font face="arial, sans-serif">Email : NWMoriarty@LBL.gov</font></div><div><font face="arial, sans-serif">Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></font></div></div><div><font face="arial, sans-serif"><span style="color:rgb(73,74,76)">ORCID : </span><font color="#494a4c"><a href="https://orcid.org/0000-0001-8857-9464" target="_blank">orcid.org/0000-0001-8857-9464</a></font></font><br></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Mar 17, 2024 at 3:53 PM Eckhard Hofmann <<a href="mailto:eckhard.hofmann@rub.de">eckhard.hofmann@rub.de</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Matt,<br>
you will have to define the appropriate occupancy groups.<br>
I usually put that into a separate file (e.g. occ.params) which you then <br>
include as input.<br>
In your case this should do the job (I think ;-)):<br>
<br>
refinement {<br>
refine {<br>
occupancies {<br>
constrained_group {<br>
selection = (chain A and resseq 802)<br>
selection = (chain W and resseq 1:6)<br>
}<br>
}<br>
}<br>
}<br>
<br>
This should refine both selections to a sum of 1.<br>
More examples are at<br>
<a href="https://phenix-online.org/documentation/reference/refinement.html#occupancy-refinement" rel="noreferrer" target="_blank">https://phenix-online.org/documentation/reference/refinement.html#occupancy-refinement</a><br>
<br>
Cheers,<br>
Eckhard<br>
<br>
Am 14.03.24 um 22:27 schrieb Matt Jordan McLeod:<br>
> Hi all,<br>
> <br>
> I am trying to navigate phenix.refine to occupancy refine a partially <br>
> occupied inhibitor vs. the waters that it displaces.<br>
> <br>
> For instance I have molecule resseq 802 in chain A, and waters 1-6 in <br>
> chain W that are overlapping. When just refining occupancy of the <br>
> molecule there are clear sites for the waters. How can I refine both <br>
> of them together so that I can get an occupancy of the molecule vs the <br>
> group of waters (which should have nearly identical occupancies)?<br>
> <br>
> Maybe, a bit more information on the differences in refinement strategy <br>
> for the occupancy vs fix occupancy vs group occupancy would be more <br>
> broadly helpful.<br>
> <br>
> I tried to make them all a group, but that didn't work as the refinement <br>
> pushed the waters out and reduced their occupancies to ~0 while leaving <br>
> the small molecule occupancy about the same as without water.<br>
> <br>
> **Waters are only placed, they are not refined), small molecule is <br>
> refined to 0.71 occupancy.**<br>
> <br>
> --<br>
> *Matthew Jordan McLeod, PhD*<br>
> Post-Doctoral Fellow |//Thorne Lab<br>
> Cornell University<br>
> G11 Physical Sciences Building<br>
> 142 Sciences Drive<br>
> Ithaca, NY 14853-3501<br>
> (607) 279 9382<br>
> <br>
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<br>
-- <br>
Prof. Dr. Eckhard Hofmann <<a href="mailto:eckhard.hofmann@rub.de" target="_blank">eckhard.hofmann@rub.de</a>><br>
Ruhr-Uni Bochum<br>
AG Proteinkristallographie<br>
ND04/318, Fachnummer 50<br>
44780 Bochum<br>
Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762<br>
ORCID: 0000-0003-4874-372X<br>
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