<div dir="ltr">Matthew<div><br></div><div>There is an "anti-LINK". Use the phil scope below. Make sure you send the mode file to Pavel and me so we can confirm that it works for you.</div><div><br></div><div>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:Monaco;color:rgb(244,244,244);background-color:rgba(0,0,0,0.85)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>exclude_from_automatic_</span><span class="gmail-s2" style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0);background-color:rgba(244,244,244,0.85)">link</span><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">ing {</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:Monaco;color:rgb(244,244,244);background-color:rgba(0,0,0,0.85)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>selection_1 = None</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:Monaco;color:rgb(244,244,244);background-color:rgba(0,0,0,0.85)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>selection_2 = None</span></p>
<p class="gmail-p1" style="margin:0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:Monaco;color:rgb(244,244,244);background-color:rgba(0,0,0,0.85)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>}</span></p></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 Fri, Jan 26, 2018 at 10:00 AM, Whitley, Matthew J <span dir="ltr"><<a href="mailto:mjw100@pitt.edu" target="_blank">mjw100@pitt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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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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