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

Yangqi Gu yangqi.gu at yale.edu
Tue Jan 21 07:35:21 PST 2020


Hi Tom,
Thank you for your detailed answers. I will try what you have suggested. I
have tried map_symmetry to find helical symmetry, but it did not give me
any reasonable answer. Is it possible to generate the NCS operator
manually? Since I know my helical symmetry, could I generate this file
manually or input somehow?
Best,
Yangqi
On Tuesday, January 21, 2020, Tom Terwilliger <
tterwilliger at newmexicoconsortium.org> wrote:

> Hi Yangqi,
>
> Assuming that your map has perfect helical symmetry, the information in
> your map is just the information for one monomer, plus information about
> contacts.
>
> With that in mind, the only information refinement can provide you about
> most of your molecule is what you get when you refine just one molecule by
> itself.   Refinement of the filament in addition will give you information
> about the contacts (by excluding bad contacts).
>
> As you note, at 3.8 A you don't have clear details about everything in the
> map.
>
> So...I suggest refining the monomer carefully as you have.  Then as you
> did, take the fixed monomer, make a filament with it, and refine with
> rigid-body refinement.
>
> Next, have a look at the contacts between monomers.  By hand, or by
> refinement of just 2 monomers, fix everything at the contacts in one
> monomer.
>
> Now make a new filament with the fixed monomer, refine rigid body
> again...etc until you have all good contacts and a filament.
>
> You might try more with finding helical symmetry in your map as well.  You
> can generate regular helical symmetry automatically with map_symmetry,
> specifying the operators. That could help as well.
>
> All the best,
> Tom T
>
> On Tue, Jan 21, 2020 at 7:32 AM BuddySphinx <yangqi.gu at yale.edu> wrote:
>
>> Hi Tom,
>>
>> Thank you for your detailed answers. I did refinement with or without NCS
>> restraints (But in both cases, I did not provide any NCS operator. So I
>> assume what it does is C1 symmetry?). Without NCS restraints refinement
>> always outperform with the NCS restraint, such as Ramachandra, bond, angle,
>> rotamer outliers. However, the biggest issue I have right now is that after
>> refinement, not every chain is identical since they were refined
>> independently? From my understanding, at the resolution I have (~3.8 A), it
>> is better to constrain them to be identical? Am I correct? I refined the
>> monomer first and then I built the model based on refined monomer.  Also,
>> for the torsion angle, do I have to specify from the command line or it is
>> already implemented in gui interface?
>>
>> 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
>>
>>
>>
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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
>> <https://www.google.com/maps/search/100+Entrada+Dr,+Los+Alamos,+NM+87544?entry=gmail&source=g>
>>
>> Email: tterwilliger at newmexicoconsortium.org
>>
>> Tel: 505-431-0010
>>
>>
>>
>>
>>
>
>
> --
> Thomas C Terwilliger
> Laboratory Fellow, Los Alamos National Laboratory
> Senior Scientist, New Mexico Consortium
> 100 Entrada Dr, Los Alamos, NM 87544
> <https://www.google.com/maps/search/100+Entrada+Dr,+Los+Alamos,+NM+87544?entry=gmail&source=g>
> Email: tterwilliger at newmexicoconsortium.org
> Tel: 505-431-0010
>
>

-- 

Yangqi Gu
Graduate Student
Malvankar Lab
Yale University, West Campus
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