<div dir="ltr">Dmitry<div><br></div><div>I suspect you will need to add some restraints but if you send me the model, I can take a look.</div><div><br clear="all"><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">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">Email : NWMoriarty@LBL.gov</font></div><div><font face="arial, sans-serif">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 Sat, Nov 4, 2023 at 1:16 PM Dmitry Semchonok <<a href="mailto:semchonok@gmail.com">semchonok@gmail.com</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"><div class="msg-5513376761157091008">
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<span lang="EN-US">Dear colleagues,<u></u> <u></u></span></p>
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<span lang="EN-US"><u></u> <u></u></span></p>
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<span lang="EN-US">While refining my model, the Mg atom for some of the margin units moves far away from them. I am also using the ELBOW files of Mg during the refinement.<u></u> <u></u></span></p>
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<span lang="EN-US"><u></u> <u></u></span></p>
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<span lang="EN-US">What is the way to restrict the movement of atoms during refinement?<u></u> <u></u></span></p>
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<span lang="EN-US">I found that this behaviour can be observed after simulated annealing is on. And the harmonic_restraints may be acquired to restrict atom movement.<u></u> <u></u></span></p>
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<span lang="EN-US">Is that right?<u></u> <u></u></span></p>
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<span lang="EN-US">I am using the GUI version of Phenix, and I cannot see those parameters.<u></u> <u></u></span></p>
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<span lang="EN-US"><u></u> <u></u></span></p>
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<span lang="EN-US">Thank you.<u></u> <u></u></span></p>
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<span lang="EN-US"><u></u> <u></u></span></p>
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<span lang="EN-US">Sincerely,<u></u> <u></u></span></p>
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<span lang="EN-US">Dmitry<u></u> <u></u></span></p>
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<span lang="EN-US"><u></u> <u></u></span></p>
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<span lang="EN-US"><u></u> <u></u></span></p>
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