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--></style></head><body lang=EN-US link=blue vlink="#954F72"><div class=WordSection1><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><o:p> </o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><o:p> </o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='border:none;padding:0in'><b>From: </b><a href="mailto:tterwilliger@newmexicoconsortium.org">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">Yangqi Gu</a>; <a href="mailto:tterwilliger@newmexicoconsortium.org">Thomas Charles Terwilliger</a><br><b>Cc: </b><a href="mailto:phenixbb@phenix-online.org">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><o:p> </o:p></p><div><div><p class=MsoNormal>Hi Yangqi,</p></div><div><p class=MsoNormal><o:p> </o:p></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><o:p> </o:p></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><o:p> </o:p></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><o:p> </o:p></p></div><div><p class=MsoNormal>Let us know if that does not do it!</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>All the best,</p></div><div><p class=MsoNormal>Tom T</p></div><div><p class=MsoNormal><o:p> </o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Mon, Jan 20, 2020 at 9:33 PM Yangqi Gu <<a href="mailto:yangqi.gu@yale.edu">yangqi.gu@yale.edu</a>> wrote:</p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;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><o:p> </o:p></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><o:p> </o:p></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><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>