<div dir="ltr">Philippe<div><br></div><div>You can use</div><div><br></div><div>apply_peptide_plane=True</div><div><br></div><div>to apply a plane to the atoms so it will be flatter regardless of the cis/trans configuration.<br><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></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Sep 11, 2023 at 7:58 AM CUNIASSE Philippe <<a href="mailto:Philippe.CUNIASSE@cea.fr">Philippe.CUNIASSE@cea.fr</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="msg8597073929622386893">
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<p class="MsoNormal"><span style="font-size:14pt">Dear all,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:14pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14pt">I am currently trying to refine a MDFF structure with the phenix RealSpaceRefine protocol of phenix.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14pt">I am wondering if it is possible to apply systematic restraints to peptide plane (in trans when they are trans and cis when they are cis in order to avoid twisted conformations of the peptide
planes at the end of the refinement.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14pt">The only possibility I saw is to apply dihedral restraints defined one by one but when having thousands of residues, it seems not really convenient.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14pt">Thanks in advance for your help.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14pt">Best regards.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14pt">Philippe.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:14pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:9pt;font-family:Courier;color:black">Philippe Cuniasse, PhD/HDR.</span><span style="font-size:13.5pt;color:black"><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:9pt;font-family:Courier;color:black">Institut de Biologie Integrative de la cellule.</span><span style="font-size:13.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9pt;font-family:Courier;color:black">UMR 9198 CNRS-CEA-Univ Paris Sud</span><span style="font-size:13.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9pt;font-family:Courier;color:black">Bat 144 CE-Saclay</span><span style="font-size:13.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9pt;font-family:Courier;color:black">91191 Gif-sur-Yvette Cedex</span><span style="font-size:13.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:9pt;font-family:Courier;color:black">France</span><span style="font-size:10.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:9pt;font-family:Courier;color:black">Tel: (33) 1 69 08 56 35</span><span style="font-size:10.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9pt;font-family:Courier;color:black">Fax: (33) 1 69 08 47 12</span><span style="font-size:10.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9pt;font-family:Courier;color:black">Email: </span><span style="font-size:9pt;font-family:Courier;color:rgb(0,0,254)"><a href="mailto:philippe.cuniasse@cea.fr" target="_blank"><span style="color:purple">philippe.cuniasse@cea.fr</span></a></span><span style="font-size:10.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9pt;font-family:Courier;color:black">Web:</span><span style="font-size:9pt;font-family:Courier;color:rgb(0,0,245)"> <a href="http://biodev.cea.fr/rasmot3d/" target="_blank"><span style="color:purple">http://biodev.cea.fr/rasmot3d/</span></a></span><span style="font-size:10.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black"><u></u> <u></u></span></p>
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