<div dir="ltr">Joel<div><br></div><div>Can you send all files directly to me.</div><div><br></div><div>NB. Any files sent to me will be held in strictest confidence.<br><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><font face="arial, sans-serif"><br></font></div><div dir="ltr"><font face="arial, sans-serif">Cheers</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Nigel</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">---</font></div><div><font face="arial, sans-serif">Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</font></div><div><font face="arial, sans-serif">Lawrence Berkeley National Laboratory</font><br><font face="arial, sans-serif">Berkeley, CA 94720-8235</font><br><font face="arial, sans-serif">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></font></div></div><div><font face="arial, sans-serif"><span style="color:rgb(73,74,76)">ORCID : </span><font color="#494a4c"><a href="https://orcid.org/0000-0001-8857-9464" target="_blank">orcid.org/0000-0001-8857-9464</a></font></font><br></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Mar 25, 2021 at 6:02 PM Joel Tyndall <<a href="mailto:joel.tyndall@otago.ac.nz">joel.tyndall@otago.ac.nz</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<p class="MsoNormal">Hi all,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">We have been finalising a structure with a ligand complexed to heme. I have been checking the close to final structure and I noticed that the ligand looks distorted away from what one would expect. We use Phenix.refine<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">We initially used the grade server for our restraints files. I also just used elbow to generate a new one. Looking at both, the restraints look reasonable (similar in both) however the initial output pdb from elbow is distorted further.
The angles /lengths looked reasonable and are similar to small molecule structures (CCDC).<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">The planarity of a bi-phenyl moiety is very distorted.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><img width="573" height="326" style="width: 5.9687in; height: 3.3958in;" id="gmail-m_-8727795448265110019Picture_x0020_1" src="cid:1786ee9c8f34cff311"><u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Are we missing something?<u></u><u></u></p>
<p class="MsoNormal">Do we need to tell phenix.refine to not over refine the model?<u></u><u></u></p>
<p class="MsoNormal">Should elbow give a distorted model?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Apologies if this is all online but my uni cant seem to access <a href="http://phenix.org" target="_blank">phenix.org</a>!<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thanks in advance<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Joel<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9pt;font-family:"Gill Sans MT",sans-serif;color:rgb(54,95,145)">Joel Tyndall |</span><span lang="EN-US" style="font-size:9pt;font-family:"Gill Sans MT",sans-serif;color:rgb(0,112,192)">
</span><span style="font-size:9pt;font-family:"Gill Sans MT",sans-serif;color:rgb(85,85,85)">BSc(Hons) PhD</span><span lang="EN-US" style="font-size:9pt;font-family:"Gill Sans MT",sans-serif"><br>
<span style="color:rgb(0,112,192)"><br>
</span><span style="color:rgb(54,95,145)">Associate Professor in Medicinal Chemistry<br>
School of Pharmacy |</span><span style="color:rgb(0,112,192)"> </span><span style="color:rgb(89,89,89)">He Rau Kawakawa</span><span style="color:rgb(0,112,192)"><br>
</span><span style="color:rgb(54,95,145)">University of Otago |</span><span style="color:rgb(0,112,192)">
</span></span><span style="font-size:9pt;font-family:"Gill Sans MT",sans-serif;color:rgb(85,85,85)">Te Whare W</span><span style="font-size:9pt;color:rgb(85,85,85)">ā</span><span style="font-size:9pt;font-family:"Gill Sans MT",sans-serif;color:rgb(85,85,85)">nanga
o Ot</span><span style="font-size:9pt;color:rgb(85,85,85)">ā</span><span style="font-size:9pt;font-family:"Gill Sans MT",sans-serif;color:rgb(85,85,85)">go<u></u><u></u></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:9pt;font-family:"Gill Sans MT",sans-serif;color:rgb(54,95,145)">Ph: 64 3 479 7293<br>
Skype: jtyndall<u></u><u></u></span></p>
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