[phenixbb] How critical is ncs operator for real space refinement

[Oleg Sobolev]

Hi Yangqi,

Yes, phenix.simple_ncs_from_pdb is the tool to search for NCS in models.
Documentation:
https://www.phenix-online.org/documentation/reference/simple_ncs_from_pdb.html

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 at 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 <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Tom Terwilliger <tterwilliger at newmexicoconsortium.org>
> *Sent: *Tuesday, January 21, 2020 9:18 AM
> *To: *Yangqi Gu <yangqi.gu at yale.edu>; Thomas Charles Terwilliger
> <tterwilliger at newmexicoconsortium.org>
> *Cc: *PHENIX user mailing list <phenixbb at phenix-online.org>
> *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 at 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
>
>
>
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>
>
>
> --
>
> Thomas C Terwilliger
>
> Laboratory Fellow, Los Alamos National Laboratory
>
> Senior Scientist, New Mexico Consortium
>
> 100 Entrada Dr, Los Alamos, NM 87544
>
> Email: tterwilliger at newmexicoconsortium.org
>
> Tel: 505-431-0010
>
>
>
>
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