<div dir="ltr">Hi Yangqi,<div><br></div><div>Yes, phenix.simple_ncs_from_pdb is the tool to search for NCS in models. Documentation:</div><div><a href="https://www.phenix-online.org/documentation/reference/simple_ncs_from_pdb.html">https://www.phenix-online.org/documentation/reference/simple_ncs_from_pdb.html</a><br></div><div><br></div><div>Also, it is available in GUI: "Select atoms" -> "NCS" -> "Find NCS" but with less options available. For matrices you'll have to run command-line.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Jan 21, 2020 at 1:17 PM BuddySphinx <<a href="mailto:yangqi.gu@yale.edu">yangqi.gu@yale.edu</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 lang="EN-US"><div class="gmail-m_1192123536492718151WordSection1"><p class="MsoNormal">Also, another question. Could I find ncs from my pdb model? I tried with map, but it failed to find the correct symmetry. Can I use phenix.simple.ncs to generate the ncs operator file?</p><p class="MsoNormal">Best,</p><p class="MsoNormal">Yangqi</p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986" target="_blank">Mail</a> for Windows 10</p><p class="MsoNormal"><u></u> <u></u></p><div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(225,225,225);padding:3pt 0in 0in"><p class="MsoNormal" style="border:none;padding:0in"><b>From: </b><a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">Tom Terwilliger</a><br><b>Sent: </b>Tuesday, January 21, 2020 9:18 AM<br><b>To: </b><a href="mailto:yangqi.gu@yale.edu" target="_blank">Yangqi Gu</a>; <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">Thomas Charles Terwilliger</a><br><b>Cc: </b><a href="mailto:phenixbb@phenix-online.org" target="_blank">PHENIX user mailing list</a><br><b>Subject: </b>Re: [phenixbb] How critical is ncs operator for real space refinement</p></div><p class="MsoNormal"><u></u> <u></u></p><div><div><p class="MsoNormal">Hi Yangqi,</p></div><div><p class="MsoNormal"><u></u> <u></u></p><div><p class="MsoNormal">You don't actually need the NCS relationships in order to refine with NCS restraints because the default is to use torsion-angle restraints which only use local relationships, not overall NCS matrices.</p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">So you can go ahead and use your rigid-body-refined starting model with torsion-angle restraints in phenix.real_space_refine. That will not impose perfect helical restraints, but I am guessing that your map already has near-perfect helical symmetry so that should not matter very much.</p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Also you might first run with just one monomer which will be much quicker and give you almost the same answer.</p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Let us know if that does not do it!</p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">All the best,</p></div><div><p class="MsoNormal">Tom T</p></div><div><p class="MsoNormal"><u></u> <u></u></p></div></div><p class="MsoNormal"><u></u> <u></u></p><div><div><p class="MsoNormal">On Mon, Jan 20, 2020 at 9:33 PM Yangqi Gu <<a href="mailto:yangqi.gu@yale.edu" target="_blank">yangqi.gu@yale.edu</a>> wrote:</p></div><blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0in 0in 0in 6pt;margin-left:4.8pt;margin-right:0in"><div><p class="MsoNormal">Dear PHENIX developers,</p><div><p class="MsoNormal">I have a question about NCS operator. Since I have a cryo-EM map and I want to refine my filament coordinates within the map. I generated the coordinate map manually in Chimera by building multiple chains with rigid body refinement. Since I did not generate the NCS operator file (I tried by doing map symmetry, it did not give me the right helical symmetry), I did not refine with ncs restraints. I am wondering in this case, how critical it is to refine a model with helical symmetry applied. Is it a must or can I go with the way I did? Hope to hear from you soon!</p></div><div><p class="MsoNormal">Best,</p></div><div><p class="MsoNormal">Yangqi<br clear="all"></p><div><p class="MsoNormal"><u></u> <u></u></p></div></div></div><p class="MsoNormal">_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br><a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></p></blockquote></div><p class="MsoNormal"><br clear="all"></p><div><p class="MsoNormal"><u></u> <u></u></p></div><p class="MsoNormal">-- </p><div><div><div><div><div><div><div><div><div><p class="MsoNormal">Thomas C Terwilliger</p><div><p class="MsoNormal">Laboratory Fellow, Los Alamos National Laboratory</p></div><div><p class="MsoNormal">Senior Scientist, New Mexico Consortium</p></div><div><p class="MsoNormal">100 Entrada Dr, Los Alamos, NM 87544</p></div><div><p class="MsoNormal">Email: <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">tterwilliger@newmexicoconsortium.org</a></p></div><div><p class="MsoNormal">Tel: 505-431-0010</p></div></div></div></div></div></div></div></div></div></div></div><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal"><u></u> <u></u></p></div></div>
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