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

Tom Terwilliger tterwilliger at newmexicoconsortium.org
Tue Jan 21 11:38:53 PST 2020

Hi Yangqi,

I gave you an incorrect answer about phenix.real_space_refinement.  Here is
Pavel's clarification:

NCS is used as constraints in real-space refinement, NCS restraints
(torsion, Cartesian) are not available in real-space refinement.

NCS copies are found automatically unless the user provides their own
selections. NCS operators are figures out internally and optionally can be

If NCS constraints are used all NCS copies will be identical after
refinement (RMSD after superposition is exactly 0).

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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