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

Tue Jan 21 07:49:23 PST 2020

Hi Yangqi,

Yes, you can generate helical operators like this:

phenix.map_symmetry helical_rot_deg=45 helical_trans_z_angstrom=4
small_map.ccp4 include_helical_symmetry=true symmetry=helical

All the best,
Tom T

On Tue, Jan 21, 2020 at 8:35 AM Yangqi Gu <yangqi.gu at yale.edu> wrote:

> 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
>
>

-- 
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
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