<div dir="ltr">Folks<div><br></div><div>phenix.refine does not use PDB LINK records as input. It is a policy decision based on LINK record (almost other things) being very easily obsoleted. It will write them if a link is found by the automatic linking algorithm or specified by an .edits file.</div><div><br></div><div>Regarding this problem, I'm happy to take a closer look if you send me the files (directly would be smartest).</div><div><br></div><div>NB. Any files sent to me will be held in strictest confidence.<br><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Jun 6, 2017 at 1:10 PM, Nikos Pinotsis <span dir="ltr"><<a href="mailto:n.pinotsis@mail.cryst.bbk.ac.uk" target="_blank">n.pinotsis@mail.cryst.bbk.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<p>there is no LINK in the input coordinates file, it was the first
I checked. <br>
</p><span class="">
<pre class="m_-851059999488354921moz-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: <a href="tel:+44%2020%207631%206827" value="+442076316827" target="_blank">+44 (0)207 631 6827</a>
F: <a href="tel:+44%2020%207631%206803" value="+442076316803" target="_blank">+44 (0)207 631 6803</a>
M: <a href="tel:+44%207923%20843593" value="+447923843593" target="_blank">+44 (0)792 384 3593</a> </pre>
</span><div><div class="h5"><div class="m_-851059999488354921moz-cite-prefix">On 06/06/2017 20:36, Tanner, John J.
wrote:<br>
</div>
<blockquote type="cite">
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><br>
</div>
<div>I think Pavel looked into the automatic linking
algorithm with my files but I never heard of a resolution to the
issue. </div>
<div><br>
<div><br>
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<blockquote type="cite">
<div>On Jun 6, 2017, at 2:22 PM, Nikos Pinotsis
<<a href="mailto:n.pinotsis@mail.cryst.bbk.ac.uk" target="_blank">n.pinotsis@mail.cryst.bbk.ac.<wbr>uk</a>>
wrote:</div>
<br class="m_-851059999488354921Apple-interchange-newline">
<div>
<div>Dear all,<br>
<br>
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>
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>
<br>
thanks in advance for any suggestions<br>
Nikos<br>
<br>
-- <br>
Dr. Nikos Pinotsis<br>
Institute of Structural and Molecular Biology<br>
Department of Biological Sciences, 3rd Floor, R313<br>
Birkbeck College<br>
Malet Street<br>
London WC1E 7HX<br>
T: <a href="tel:+44%2020%207631%206827" value="+442076316827" target="_blank">+44 (0)207 631 6827</a><br>
F: <a href="tel:+44%2020%207631%206803" value="+442076316803" target="_blank">+44 (0)207 631 6803</a><br>
M: <a href="tel:+44%207923%20843593" value="+447923843593" target="_blank">+44 (0)792 384 3593</a><br>
<br>
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