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Hi Matthew,<br>
<br>
could you please send me PDB file before and after refinement
(please make sure not to send files to the entire phenixbb) and the
data file? I'd like to reproduce and investigate this. Then I'll see
what's best to do in this case..<br>
<br>
Thanks,<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 1/26/18 10:00, Whitley, Matthew J
wrote:<br>
</div>
<blockquote type="cite"
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<p style="margin-top:0;margin-bottom:0">Hello all,</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">I am currently refining
a structure using Phenix 1.13-2998.� Present in this structure
is a diphosphate-containing ligand.� In the protein chain
surrounding the binding site, there is an arginine side chain
that points generally toward the diphosphate group, but I
cannot define the specific location of the side chain because
the side chain density is very poor.� The density for the
ligand is unambiguous. �Upon refinement, Phenix places the Arg
side chain so close to the ligand that it draws a covalent
bond between the two, and the post-refinement PDB file
contains a LINK record for this bond.� In reality, the two are
not covalently connected, and ideally Phenix would find a
conformation for this side chain that is outside of covalent
bonding distance.� I have tried refining after manually moving
the side-chain to a non-clashing position multiple times, but
in every case the output PDB contains a LINK for a covalent
bond between ligand and side chain.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">My question: How can I
tell Phenix NOT to allow these atoms to come with covalent
bonding distance?� Is there some kind of "anti-LINK"
information I can feed it that will force phenix.refine to
select some other conformation for the side chain?<br>
</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Thanks for your advice.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Sincerely,</p>
<p style="margin-top:0;margin-bottom:0">Matthew Whitley<br>
</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
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---
<div>Matthew J. Whitley, Ph.D.</div>
<div>Research Instructor</div>
<div>Department of Pharmacology & Chemical Biology</div>
<div>University of Pittsburgh School of Medicine</div>
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<br>
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