<div dir="ltr"><div dir="ltr">Hi Yangqi,</div><div dir="ltr"><br><div>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.</div><div><br></div><div>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.</div><div><br></div><div>Also you might first run with just one monomer which will be much quicker and give you almost the same answer.</div><div><br></div><div>Let us know if that does not do it!</div><div><br></div><div>All the best,</div><div>Tom T</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Jan 20, 2020 at 9:33 PM Yangqi Gu <<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 dir="ltr">Dear PHENIX developers,<div>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!</div><div>Best,</div><div>Yangqi<br clear="all"><div><br></div></div></div>
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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Thomas C Terwilliger<div>Laboratory Fellow, Los Alamos National Laboratory</div><div>Senior Scientist, New Mexico Consortium</div><div>100 Entrada Dr, Los Alamos, NM 87544</div><div>Email: <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">tterwilliger@newmexicoconsortium.org</a></div><div>Tel: 505-431-0010</div><div><br></div></div></div></div></div></div></div></div></div></div></div>