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

Tom Terwilliger tterwilliger at newmexicoconsortium.org
Tue Jan 21 06:20:54 PST 2020

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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