<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hello,<br>
<br>
this error means your input PDB file contains atoms that nearly
perfectly overlap. It is best if you inspect the PDB file and
resolve the issues.<br>
<br>
Answering your question:<br>
<br>
In phenix.refine GUI :<br>
<br>
Refinement settings -> All parameters -> Search parameters<br>
<br>
paste nonbonded_distance_threshold and hit Enter. In popped window
replace default 0.5 with an empty line and save.<br>
<br>
Alternatively, you can save one line<br>
<br>
refinement.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None<br>
<br>
into a file and give this file to phenix.refine along with all other
file (PDB, reflections, etc).<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 1/1/15 7:22 PM, Wind Sui wrote:<br>
</div>
<blockquote
cite="mid:1909039909.2104817.1420168968945.JavaMail.yahoo@jws10076.mail.ne1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, Sans-Serif;font-size:12px">
<div id="yui_3_16_0_1_1420167744018_5420" dir="ltr">Dear All,</div>
<div id="yui_3_16_0_1_1420167744018_5420" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1420167744018_5420" dir="ltr">I use the
graphic phenix.refine to do a refinement, and Phenix informed
me I need to have a command
"refinement.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None".
Will you please tell me by graphic phenic.refine, how can I
input this command?</div>
<div id="yui_3_16_0_1_1420167744018_5420" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1420167744018_5420" dir="ltr">Wind</div>
<div id="yui_3_16_0_1_1420167744018_5420" dir="ltr" class=""
style="">�</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>
</pre>
</blockquote>
<br>
</body>
</html>