<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<style><!--
/* Font Definitions */
@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:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.E-MailFormatvorlage17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 2.0cm 70.85pt;}
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]-->
</head>
<body lang="EN-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span lang="DE" style="color:#1F497D">Dear colleagues,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">I am trying to refine a protein-DNA complex. In this structure, 2 DNA double strands are present with 50% occupancy (or similar occupancy’s) and overlap at certain positions. Phenix.refine crashed due to a nonbonded
interaction distance issue. To fix that, I tried to exclude the DNA strands using:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1F497D">pdb_interpretation {<br>
custom_nonbonded_symmetry_exclusions="chain E"<br>
custom_nonbonded_symmetry_exclusions="chain F"<br>
}<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Nevertheless, phenix.refine crashed with the same error message. Changing the “<b>nonbonded_distance_threshold</b>” works, but results in terrible statistics (since this applies for the complete structure, I
guess). <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Is there a way to exclude only the DNA strands (in regard to the clash guard) or a similar approach to refine the structure?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Thank you in advance for your help,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Tobias<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<br>
<hr>
<font face="Arial" color="Gray" size="2"><br>
Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de<br>
Das HZI ist seit 2007 zertifiziertes Mitglied im "<b>audit</b> beruf<b>und</b>familie"<br>
50 Jahre Spitzenforschung - 50 Jahre HZI: www.helmholtz-hzi.de/50<br>
<br>
Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung<br>
Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur<br>
Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer<br>
Gesellschaft mit beschränkter Haftung (GmbH)<br>
Sitz der Gesellschaft: Braunschweig<br>
Handelsregister: Amtsgericht Braunschweig, HRB 477<br>
</font>
</body>
</html>