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<p>Sorry, I don't use biopython. You should submit a bug with
biopython, or better yet, fix it, and submit a patch :-). The
entity_poly_seq mmCIF table is roughly equivalent to the PDB
SEQRES records.<br>
</p>
<p>Also, why use mmCIF? If biopython's PDB writer is better, then
use it. Chimera's PDB reader is much faster than its mmCIF
reader. ChimeraX's mmCIF reader is faster than its PDB reader (at
least it was, haven't measured recently). If you need to convert
a PDB file to an mmCIF file, try using ChimeraX,
<a class="moz-txt-link-freetext" href="http://www.rbvi.ucsf.edu/chimerax/">http://www.rbvi.ucsf.edu/chimerax/</a>. And if you find a mmCIF bug in
ChimeraX, submit a bug report and we'll fix it.<br>
</p>
<p> HTH,</p>
<p> Greg<br>
</p>
<div class="moz-cite-prefix">On 1/21/2019 2:49 AM, Carmen San Martin
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CABK2RzXZvG5S-kZrS89mbkrH_c3ok=YuQRn3gf7_J4M3yp4PeA@mail.gmail.com">
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<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>
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data-smartmail="gmail_signature">
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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"
moz-do-not-send="true">carmen@cnb.csic.es</a><br>
Phone: 34-91-5855450<br>
Fax: 34-91-5854506<br>
<a
href="http://tinyurl.com/carmensanmartinlab"
target="_blank"
moz-do-not-send="true">http://tinyurl.com/carmensanmartinlab</a><br>
</div>
<div> <a
href="https://sites.google.com/site/adenonet/"
target="_blank"
moz-do-not-send="true">https://sites.google.com/site/adenonet/</a>
<br>
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<div dir="ltr" class="gmail_attr">On Fri, Jan 18, 2019 at 5:44
PM Greg Couch <<a href="mailto:gregc@cgl.ucsf.edu"
moz-do-not-send="true">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>
</div>
<blockquote type="cite">
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<div dir="ltr">
<div dir="ltr">
<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>
</div>
<div class="gmail_default"
style="font-family:arial,helvetica,sans-serif">Best,<br>
</div>
<div>
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class="gmail-m_-7383102150271839751gmail_signature">
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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"
moz-do-not-send="true">carmen@cnb.csic.es</a><br>
Phone: 34-91-5855450<br>
Fax: 34-91-5854506<br>
<a
href="http://tinyurl.com/carmensanmartinlab"
target="_blank"
moz-do-not-send="true">http://tinyurl.com/carmensanmartinlab</a><br>
</div>
<div> <a
href="https://sites.google.com/site/adenonet/"
target="_blank"
moz-do-not-send="true">https://sites.google.com/site/adenonet/</a>
<br>
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