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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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          style="font-family:arial,helvetica,sans-serif">Hi Greg,</div>
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          style="font-family:arial,helvetica,sans-serif"><br>
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        <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>
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        <div class="gmail_default"
          style="font-family:arial,helvetica,sans-serif">Best,<br>
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                                  <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"
                                      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>
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      <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"
            moz-do-not-send="true">gregc@cgl.ucsf.edu</a>> wrote:<br>
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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>
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                      style="font-family:arial,helvetica,sans-serif"><br>
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                    <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>
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                      style="font-family:arial,helvetica,sans-serif">Best,<br>
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                                              <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"
                                                  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>
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                                                  href="https://sites.google.com/site/adenonet/"
                                                  target="_blank"
                                                  moz-do-not-send="true">https://sites.google.com/site/adenonet/</a>
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