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    <p>there is no LINK in the input coordinates file, it was the first
      I checked. <br>
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    <pre class="moz-signature" cols="72">Dr. Nikos Pinotsis
Institute of Structural and Molecular Biology
Department of Biological Sciences, 3rd Floor, R313
Birkbeck College
Malet Street
London WC1E 7HX
T: +44 (0)207 631 6827
F: +44 (0)207 631 6803
M: +44 (0)792 384 3593 </pre>
    <div class="moz-cite-prefix">On 06/06/2017 20:36, Tanner, John J.
      wrote:<br>
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      I had a similar problem in Feb. 2017 with a sulfate ion running
      into a flavin. It turned out the PDB file mistakenly had a “LINK”
      line forcing a covalent bond where there should not have been one.
      I deleted the LINK line from the PDB file and everything was
      fine. 
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      <div class="">I think Pavel looked into the automatic linking
        algorithm with my files but I never heard of a resolution to the
        issue. </div>
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                          John J. Tanner<br class="">
                          Professor of Biochemistry and Chemistry</div>
                        <div style="color: rgb(0, 0, 0); font-family:
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                          Chair, Biochemistry Department Graduate
                          Admissions Committee </div>
                        <div style="color: rgb(0, 0, 0); font-family:
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                          Department of Biochemistry</div>
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                          University of Missouri-Columbia<br class="">
                          117 Schweitzer Hall</div>
                        <div class="">503 S College Avenue<br class="">
                          Columbia, MO 65211<br class="">
                          Phone: 573-884-1280</div>
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                          Fax: 573-882-5635<br class="">
                          Email: <a moz-do-not-send="true"
                            href="mailto:tannerjj@missouri.edu" class="">tannerjj@missouri.edu</a><br
                            class="">
                          <a moz-do-not-send="true"
                            href="http://faculty.missouri.edu/%7Etannerjj/tannergroup/tanner.html"
                            class="">http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html</a></div>
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                          Lab: Schlundt Annex rooms 3,6,9, 203B, 203C</div>
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                          Office: Schlundt Annex 203A</div>
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            <blockquote type="cite" class="">
              <div class="">On Jun 6, 2017, at 2:22 PM, Nikos Pinotsis
                &lt;<a moz-do-not-send="true"
                  href="mailto:n.pinotsis@mail.cryst.bbk.ac.uk" class="">n.pinotsis@mail.cryst.bbk.ac.uk</a>&gt;
                wrote:</div>
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              <div class="">
                <div class="">Dear all,<br class="">
                  <br class="">
                  I have a protein-ligand structure with several chains
                  in the AU. After refinement one of the ligands forms a
                  close contact 1.8A with the protein. For the rest of
                  the protein-ligand chains the same interaction is as
                  expected to 2.7-2.8 A forming an H-bond. I tried to
                  adjust this ligand with coot but everytime I am
                  getting back the same 1.8 A close contact. There is
                  enough density for the ligand and I can even see that
                  it can fit better to distance 2.4-2.5A H-bond with the
                  protein<br class="">
                  Is there a way to constrain this distance to more than
                  2A? Should I fix the ligand atom that interacts?
                  Unless I am missing something more fundamental. The
                  ligand cif file is the default in phenix, the data set
                  is a quite decent 2.3A.<br class="">
                  <br class="">
                  thanks in advance for any suggestions<br class="">
                  Nikos<br class="">
                  <br class="">
                  -- <br class="">
                  Dr. Nikos Pinotsis<br class="">
                  Institute of Structural and Molecular Biology<br
                    class="">
                  Department of Biological Sciences, 3rd Floor, R313<br
                    class="">
                  Birkbeck College<br class="">
                  Malet Street<br class="">
                  London WC1E 7HX<br class="">
                  T: +44 (0)207 631 6827<br class="">
                  F: +44 (0)207 631 6803<br class="">
                  M: +44 (0)792 384 3593<br class="">
                  <br class="">
                  _______________________________________________<br
                    class="">
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