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

[Yangqi Gu]

Hi Tom and Pavel,
Thank you for your help. I think I have a much better understanding what I
should do now. I will try with your suggestions and I will let you know.
Best,
Yangqi

On Tue, Jan 21, 2020 at 2:39 PM Tom Terwilliger <
tterwilliger at newmexicoconsortium.org> wrote:

> 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
> refined.
>
> 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
>
>

-- 

Yangqi Gu
Graduate Student
Malvankar Lab
Yale University, West Campus
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