<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body text="#000000" bgcolor="#FFFFFF">
Hi Aaron,<br>
<br>
exclude that side chain from non-bonded repulsion with the symmetry
mate by using<br>
<br>
custom_nonbonded_symmetry_exclusions="chain A and resseq 123 and
sidechain"<br>
<br>
If using CL simply add the above parameter (after editing the
selection appropriately). If using GUI, find this parameter in "All
parameters" and type in atom selection.<br>
<br>
Let me know if you have any questions or problems doing this!<br>
<br>
Also, could you please send me the PDB file off-list (or just a part
of it containing that residue)? I'd like to automate this in
phenix.refine so that in future the program takes care of this
automatically.<br>
<br>
Thanks,<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 2/1/18 14:00, Keller, Jacob wrote:<br>
</div>
<blockquote type="cite"
cite="mid:D59BFC92F3D19A49B02F9A40433D335D01E25BEDF2@JFMB1.hhmi.org">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered
medium)">
<!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]-->
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
p.msonormal0, li.msonormal0, div.msonormal0
{mso-style-name:msonormal;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="WordSection1">
<p class="MsoNormal">Model two conformations?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">JPK<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal"><span style="font-family:"Courier
New"">+++++++++++++++++++++++++++++++++++++++++++++++++<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier
New"">Jacob Pearson Keller<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier
New"">Research Scientist / Looger Lab<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier
New"">HHMI Janelia Research Campus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier
New";color:#222222;background:white">19700 Helix Dr,
Ashburn, VA 20147</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New";color:#222222;background:white">Desk:
(571)209-4000 x3159<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier
New";color:#222222;background:white">Cell:
(301)592-7004<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier
New";color:#222222;background:white">+++++++++++++++++++++++++++++++++++++++++++++++++</span><span
style="font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New";color:#222222;background:white">The content of
this email is confidential and intended for the recipient
specified in message only. It is strictly forbidden to
share any part of this message with any third party,
without a written consent of the sender. If you received
this message by mistake, please reply to this message and
follow with its deletion, so that we can ensure such a
mistake does not occur in the future.<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>
[<a class="moz-txt-link-freetext" href="mailto:phenixbb-bounces@phenix-online.org">mailto:phenixbb-bounces@phenix-online.org</a>]
<b>On Behalf Of </b>Aaron Oakley<br>
<b>Sent:</b> Thursday, February 1, 2018 4:37 AM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> [phenixbb] side-chain on special position.<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hello fellow Phenix-ers, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I have a structure I am trying to finish
in Phenix.refine<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">The is one problem: a glutamate residue
sitting on a crystallography 2-fold axis<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">with partial occupancy (picture
attached). This residue and its symmetry mate appear to take
turns sitting<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">at this position: filling the density
leads to severe collision with its symmetry mate.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Building the side-chain with occupancy
0.5 doesn’t seem to help, as the residue is pushed<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">out of density during refinement.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Any work-arounds?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Thanks all,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Aaron<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><img style="width:5.0625in;height:5.0in"
id="_x0034_6F39796-9CBF-42C3-BE1D-1107FC78D904"
src="cid:part1.C64911A0.BF8407C0@lbl.gov" class=""
height="480" width="486"><o:p></o:p></p>
</div>
</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>
Unsubscribe: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a></pre>
</blockquote>
<br>
</body>
</html>