<html>
<head>
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
</head>
<body>
<p>Phenix used to have, and maybe still does, a problem with
generating mmCIF files. In several places, it outputted the author
sequence number, auth_seq_id, where it should put the label
sequence number, label_seq_id. Tristan Croll has already reported
one version of this bug to Phenix about 5 months ago,
<a class="moz-txt-link-freetext" href="https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2483">https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2483</a>. Perhaps
there is a newer version of Phenix that has the bug fixed? And is
that the mistake you make when you generate the mmCIF from the PDB
file yourself? You should be able to tell by looking at the
atom_site table and the label_seq_id's for the various residues
and see how that matches up to the beg_label_seq_id and
end_label_seq_id values in the struct_conf table. The size of the
complex is not an issue. If that's not the bug, then send me the
complete mmCIF file and I'll guess what the bug is.<br>
</p>
<p><br>
</p>
<p> HTH,<br>
</p>
<p> </p>
<p> Greg<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 3/4/2020 12:58 AM, Tetter Stephan
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:4beb95726b8c4e23b95b1b95bfda13af@org.chem.ethz.ch">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
<div id="divtagdefaultwrapper"
style="font-size:12pt;color:#000000;font-family:Calibri,Helvetica,sans-serif;"
dir="ltr">
<br>
<div style="color: rgb(0, 0, 0);">Dear all,<br>
<div>
<div id="divtagdefaultwrapper" dir="ltr"
style="font-size:12pt; color:#000000;
font-family:Calibri,Helvetica,sans-serif">
<p><br>
</p>
<p>I am having an issue with secondary structure display.
I am real-space refining a set of 120 chains in phenix.
Of these, only 10 are unique, the rest is
symmetry-related. Thus, I define secondary structure
elements for the 10 unique chains only. The output pdb
file header contains the secondary structure elements as
imposed during refinement. Displaying this pdb file in
ChimeraX shows the right secondary structure. The mmcif
file instead, whether I use the phenix output or
generate it from the pdb myself, displays different,
non-sensical structures. Secondary structure is shown in
loop regions, and some actual strands and helices not
recognized at all. This artifact is only shown for the
10 subunits with secondary structure definitions, the
other subunits show no secondary structure at all, thus
something is read in, but not correctly, apparently. Any
idea what the problem could be? Could the size of the
complex be an issue?</p>
<p><br>
</p>
<p>The attachments show the lines from the two file types
concerning secondary structure definitions.
<br>
</p>
<p><br>
</p>
<p>Kind regards, <br>
</p>
<p><br>
</p>
<p>Stephan <br>
</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
</div>
</div>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
ChimeraX-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:ChimeraX-users@cgl.ucsf.edu">ChimeraX-users@cgl.ucsf.edu</a>
Manage subscription:
<a class="moz-txt-link-freetext" href="http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a>
</pre>
</blockquote>
</body>
</html>