<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">Yep, this is not too surprising since
the current phenix.refine implementation of rotamer fitting does
not use the new residue/rotamer fitting machinery (the one I
showed at past WCPCW), which will be in place in a few coming
months. Stay tuned!<br>
<br>
Pavel<br>
<br>
On 4/19/13 7:27 PM, Rongjin wrote:<br>
</div>
<blockquote cite="mid:tencent_7C735827634FABBE404E9007@qq.com"
type="cite">Hi Nat, <br>
<br>
You are right. By turning off the "fix rotamers" the Arg does not
move any more.<br>
<br>
Best<br>
<br>
Rongjin <br>
<div>
<div><br>
</div>
<div><br>
</div>
<div style="font-size: 12px;font-family: Arial
Narrow;padding:2px 0 2px 0;">------------------ Original ------------------</div>
<div style="font-size: 12px;background:#efefef;padding:8px;">
<div><b>From: </b> "Nathaniel Echols"<a class="moz-txt-link-rfc2396E" href="mailto:nechols@lbl.gov"><nechols@lbl.gov></a>;</div>
<div><b>Date: </b> Apr 20, 2013</div>
<div><b>To: </b> "PHENIX user mailing
list"<a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a>; <wbr></div>
<div><b>Subject: </b> Re: [phenixbb] how to fix a side chain
not to be refined?</div>
</div>
<div><br>
</div>
On Fri, Apr 19, 2013 at 2:14 PM, Rongjin
<a class="moz-txt-link-rfc2396E" href="mailto:guanrj@foxmail.com"><guanrj@foxmail.com></a> wrote:<br>
> I have an Arg with flexible side chain, close to an iodide
ion. Every time<br>
> I refine it, the side chain of Arg will push the iodide ion
away, even I<br>
> selected<br>
<br>
The syntax below looks correct to me, although you should
probably do<br>
the same thing for the ADP selection, but it's a little
disturbing<br>
that it's doing this. Do you have rotamer correction turned
on? That<br>
may be the problem, if it is trying to fit to the difference
density<br>
(I don't think it's very aware of nearby atoms).<br>
<br>
-Nat<br>
<br>
> the Arg not to be refined:<br>
><br>
> refine {<br>
> strategy = *individual_sites
individual_sites_real_space rigid_body \<br>
> *individual_adp group_adp tls *occupancies
group_anomalous<br>
> sites {<br>
> individual = "not (chain A and resid 40)"<br>
> }<br>
> }<br>
><br>
><br>
> The residue 40 in Chain A is that Arg close to the Iodide.
Is this selection<br>
> correct?<br>
> How to fix the side chain of Arg in refinement?<br>
><br>
> I attached two pictures, one before and one after
refinement, the local area<br>
> of the Arg<br>
> and the iodide. The iodide is bound to an Asn residue of
one symmetric<br>
> molecule.<br>
><br>
> Thank you<br>
> Rongjin Guan<br>
><br>
><br>
><br>
> _______________________________________________<br>
> phenixbb mailing list<br>
> <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
> <a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
><br>
_______________________________________________<br>
phenixbb mailing list<br>
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
.<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<br>
</body>
</html>