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

[Pavel Afonine]

Hi Yangqi,

it depends what you call "worse" and also keep in mind that clashscore 
is not the only metric of success. Some metrics get get worse and some 
better, and changes in some may be just fine and some may indicate problems.
It's hard to comment meaningfully based upon rather scarce amount of 
information you provide.
I can have a look if you share (off list!) map, models (input and 
output) and the log file from refinement.

Pavel

On 1/21/20 17:19, Yangqi Gu wrote:
> Thank you Tom and Oleg. I tried refinement as you suggested. I did 
> local refinement after I did the rigid body. However, the first couple 
> of cycles, the clashscore and everything (statistics) seems improved, 
> but then getting worse after more cycles. I did both 5 and 10 cycles, 
> the final outputs are all worse than what I started with, which means 
> only after rigid body fitting. Is this normal?
> Best,
> Yangqi
>
> On Tue, Jan 21, 2020 at 5:32 PM Oleg Sobolev <osobolev at lbl.gov 
> <mailto:osobolev at lbl.gov>> wrote:
>
>     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
>     <mailto: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
>         <mailto:tterwilliger at newmexicoconsortium.org>
>         *Sent: *Tuesday, January 21, 2020 9:18 AM
>         *To: *Yangqi Gu <mailto:yangqi.gu at yale.edu>; Thomas Charles
>         Terwilliger <mailto:tterwilliger at newmexicoconsortium.org>
>         *Cc: *PHENIX user mailing list <mailto: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
>         <mailto: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
>         <mailto:tterwilliger at newmexicoconsortium.org>
>
>         Tel: 505-431-0010
>
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>
>
> -- 
>
> Yangqi Gu
> Graduate Student
> Malvankar Lab
> Yale University, West Campus
>
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