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

[Yangqi Gu]

Hi Pavel,
I sent you a separate email with all the files. Thank you very much for
your help!
Best,
Yangqi

On Tue, Jan 21, 2020 at 8:31 PM Pavel Afonine <pafonine at lbl.gov> wrote:

> 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> 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
>>>
>>>
>>>
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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
>>>
>>> Tel: 505-431-0010
>>>
>>>
>>>
>>>
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>>
>>
>
> --
>
> Yangqi Gu
> Graduate Student
> Malvankar Lab
> Yale University, West Campus
>
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>
>

-- 

Yangqi Gu
Graduate Student
Malvankar Lab
Yale University, West Campus
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