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

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 < [email protected]> 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 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: [email protected] Tel: 505-431-0010

-- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus