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

Yangqi Gu yangqi.gu at yale.edu
Tue Jan 21 17:19:29 PST 2020


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> 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> 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 <tterwilliger at newmexicoconsortium.org>
>> *Sent: *Tuesday, January 21, 2020 9:18 AM
>> *To: *Yangqi Gu <yangqi.gu at yale.edu>; Thomas Charles Terwilliger
>> <tterwilliger at newmexicoconsortium.org>
>> *Cc: *PHENIX user mailing list <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> 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
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
>>
>>
>>
>>
>> --
>>
>> 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
>>
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
>
>

-- 

Yangqi Gu
Graduate Student
Malvankar Lab
Yale University, West Campus
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20200121/d04c0567/attachment.htm>


More information about the phenixbb mailing list