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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="moz-cite-prefix">On 1/18/2019 4:06 AM, Carmen San Martin
      wrote:<br>
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cite="mid:CABK2RzX8GZFWrw9Au3tej2ZkvMH8ZET4hpRhYL0BHVvhMowBLQ@mail.gmail.com">
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              style="font-family:arial,helvetica,sans-serif">Hi all,</div>
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              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>
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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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            <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>
                                        <br>
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      <pre class="moz-quote-pre" wrap="">_______________________________________________
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