<div dir="ltr"><div dir="ltr"><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><font face="arial, sans-serif">Joel</font></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">I would suggest you update to 1.19.2 or later at</font></div><div><div dir="ltr"><div class="gmail_extra"><div dir="ltr"><div class="gmail_extra"><br></div><div class="gmail_extra"><a href="http://www.phenix-online.org/download/nightly_builds.cgi" target="_blank">http://www.phenix-online.org/download/nightly_builds.cgi</a><br></div><div class="gmail_extra"><br></div></div></div></div></div></div></div></div></div></div></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div lang="EN-NZ" style="overflow-wrap: break-word;"><div class="gmail-m_4950990631099289672WordSection1"><br>
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<p class="MsoNormal">It has been a while since we have done much with phenix. We are refining a structure with a known ligand, voriconazole (exists on the pdb). We get an error regarding a lack of .cif file/restraints.</p></div></div></blockquote><div><br></div><div>You need to supply a restraints file (CIF format) for some ligands in Phenix.</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div lang="EN-NZ" style="overflow-wrap: break-word;"><div class="gmail-m_4950990631099289672WordSection1"><p class="MsoNormal"><u></u><u></u></p>
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<p class="MsoNormal">Do we normally need to specify a cif file given this is a known ligand and can be retrieved in Coot?</p></div></div></blockquote><div><br></div><div>No not normally, only those retraints that Phenix does not have in the distributed library. Coot does not retrieve restraints, rather information.</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div lang="EN-NZ" style="overflow-wrap: break-word;"><div class="gmail-m_4950990631099289672WordSection1"><p class="MsoNormal"><u></u><u></u></p>
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<p class="MsoNormal">I assume that phenix would call on a known library of ligands/monomers that are known. Is this the correct library?<u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">phenix-installer-1.17.1-3660-intel-windows-x86_64\modules\chem_data\chemical_components\</span></p></div></div></blockquote><div><br></div><div>No, this is a library of CIF files that contain information not restraints. eLBOW can create restraints from these files using the --chemical_component option.</div><div><br></div><div>You can learn more on the Phenix Tutorials Youtube channel.</div><div><br></div><div><a class="gmail-reference external" href="https://www.youtube.com/c/phenixtutorials" style="font-family:Verdana,Helvetica,Arial,sans-serif;font-size:16px">www.youtube.com/c/phenixtutorials</a></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div lang="EN-NZ" style="overflow-wrap: break-word;"><div class="gmail-m_4950990631099289672WordSection1"><p class="MsoNormal"><span style="font-size:12pt;color:black"><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Many thanks<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:12pt;color:black">Joel</span><u></u><u></u></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)">Joel Tyndall |</span><span lang="EN-US" style="font-size:9pt;font-family:"Gill Sans MT",sans-serif;color:rgb(0,112,192)">
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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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