Hi Yangqi,Yes, phenix.simple_ncs_from_pdb is the tool to search for NCS in models. Documentation: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.Best regards,Oleg Sobolev.On Tue, Jan 21, 2020 at 1:17 PM BuddySphinx <yangqi.gu@yale.edu> wrote:_______________________________________________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?
Best,
Yangqi
Sent from Mail for Windows 10
From: Tom Terwilliger
Sent: Tuesday, January 21, 2020 9:18 AM
To: Yangqi Gu; Thomas Charles Terwilliger
Cc: PHENIX user mailing list
Subject: Re: [phenixbb] How critical is ncs operator for real space refinement
Hi Yangqi,
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.
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.
Also you might first run with just one monomer which will be much quicker and give you almost the same answer.
Let us know if that does not do it!
All the best,
Tom T
On Mon, Jan 20, 2020 at 9:33 PM Yangqi Gu <yangqi.gu@yale.edu> wrote:
Dear PHENIX developers,
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!
Best,
Yangqi
_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave@phenix-online.org
--
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Tel: 505-431-0010
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave@phenix-online.org