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<p>there is no LINK in the input coordinates file, it was the first
I checked. <br>
</p>
<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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cite="mid:DC1950B4-50B6-470D-82E4-8393A9CEB955@missouri.edu"
type="cite">
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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.�
<div class=""><br class="">
</div>
<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>
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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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<br class="">
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<blockquote type="cite" class="">
<div class="">On Jun 6, 2017, at 2:22 PM, Nikos Pinotsis
<<a moz-do-not-send="true"
href="mailto:n.pinotsis@mail.cryst.bbk.ac.uk" class="">n.pinotsis@mail.cryst.bbk.ac.uk</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<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="">
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