<div dir="ltr"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Hi Greg,</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">you are correct, we do not have entity_poly_seq. We are using biopython for the conversion, but we have not been able to figure out how to create that particular table. Any hints will be welcome!</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Best,<br></div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div> -------------------------------------------------------------<br> Carmen San Martín, Ph. D. <br> Centro Nacional de Biotecnología (CNB-CSIC)<br> Darwin, 3<br> 28049-Madrid (SPAIN)<br> Email: <a href="mailto:carmen@cnb.csic.es" target="_blank">carmen@cnb.csic.es</a><br> Phone: 34-91-5855450<br> Fax: 34-91-5854506<a href="http://www.cnb.csic.es/" target="_blank"></a><br> <a href="http://tinyurl.com/carmensanmartinlab" target="_blank">http://tinyurl.com/carmensanmartinlab</a><br></div><div> <a href="https://sites.google.com/site/adenonet/" target="_blank">https://sites.google.com/site/adenonet/</a> <br></div><div> ------------------------------------------------------------</div></div></div></div></div></div></div></div></div></div></div></div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Jan 18, 2019 at 5:44 PM Greg Couch <<a href="mailto:gregc@cgl.ucsf.edu">gregc@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<p>The PDB file is being incorrectly converted to a mmCIF file.
Without seeing the two files, I can not say for sure, but it is
mostly like that the entity_poly_seq table is missing or
incomplete. Chimera uses the auth_seq_id to identify the
residues, but uses label_seq_id to connect the residues. So if
the sequence for the gap residues is missing, and the
label_seq_id's are consecutive, then the residues are adjacent,
i.e, connected.</p>
<p>What program is doing the PDB to mmCIF conversion?<br>
</p>
<p> HTH,</p>
<p> Greg<br>
</p>
<div class="gmail-m_-7383102150271839751moz-cite-prefix">On 1/18/2019 4:06 AM, Carmen San Martin
wrote:<br>
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<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Hi all,</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">I am using
chimera to display a structure with a 10-residue gap. When
I use a pdb format file, the gap appears as a dashed line
and everything is fine. However, when I convert the
coordinate file to cif format, chimera draws a very long
bond across the gap. Further, the residue numbering seems
to have changed, so that now instead of skipping the 10
figures in the gap, the residues at both sides are
consecutively numbered, and therefore the numbering in the
rest of the protein is wrong. I understand this happens
because chimera is using the cif column "label_seq_id"
instead of "auth_seq_id" to identify the residue number.
Is there a way to make chimera use the auth_seq_id column
instead?</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Sorry if
this has already been answered, I googled it and saw
similar questions but not the actual answer to this one.</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
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<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Best,<br>
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-------------------------------------------------------------<br>
Carmen San Martín, Ph. D. <br>
Centro Nacional de
Biotecnología (CNB-CSIC)<br>
Darwin, 3<br>
28049-Madrid (SPAIN)<br>
Email: <a href="mailto:carmen@cnb.csic.es" target="_blank">carmen@cnb.csic.es</a><br>
Phone: 34-91-5855450<br>
Fax: 34-91-5854506<br>
<a href="http://tinyurl.com/carmensanmartinlab" target="_blank">http://tinyurl.com/carmensanmartinlab</a><br>
</div>
<div> <a href="https://sites.google.com/site/adenonet/" target="_blank">https://sites.google.com/site/adenonet/</a>
<br>
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