[phenixbb] question about constrain ncs

Pavel Afonine PAfonine at lbl.gov
Tue Oct 6 09:46:07 PDT 2009


Hi Jon,

try this:

- run phenix.refine with NCS restraints and use "optimize_wxc=true" 
(just out of curiosity, try w/o this option). Try these strategies to 
see which one works best: "strategy=individual_sites+group_adp+tls"  or 
"strategy=individual_sites+individual_adp+tls" (don't forget to specify 
TLS groups. How?  It is a separate question).

- run CNS or Refmac (whatever you like) using NCS constraints.

Compare Rwork, Rfree and Rfree-Rwork, map CC for each residue 
(phenix.real_space_correlation), and then you have a conclusive answer. 
Everything else are speculations -:)

Answering your question - yes, NCS constraints are in (my ?) to-do list.

I would appreciate if you share the results of the above experiment with 
me. And I'm open for further discussion.

All the best!
Pavel.


On 10/6/09 6:55 AM, Jonathan Grimes wrote:
> Pavel Afonine wrote:
>> Hi,
>>
>> phenix.refine model.pdb data.mtz main.ncs=true
>>
>> will do refinement with NCS restraints. The NCS groups will be 
>> determined automatically. It may be important to check the automatic 
>> choice.
>> See phenix.refine manual for details:
>> http://phenix-online.org/documentation/refinement.htm#anch24
>>
>> Also, at this resolution you may consider using TLS and/or group ADP 
>> refinement.
>>
>> phenix.refine does not have NCS constrains, which I believe you do 
>> not need at this resolution.
>>
>> Pavel.
>>
>>
>   Hi Pavel,
>
>    Got to disagree with you on this one.  Depends on your obs to 
> params.  If youve
>    got 90% solvent then perhaps.......I would always favour reducing 
> my params by
>    a factor of 5 at 3.6Angs.
>
>   Jon 
>
>   PS  Any plans for coding up NCS constraints !!!   ;-)
>
>
>
> -- 
> Dr. Jonathan M. Grimes,   
> University Research Lecturer
> Division of Structural Biology
> Wellcome Trust Centre for Human Genetics
> University of Oxford
> Roosevelt Drive,
> Oxford OX3 7BN, UK
>
> Email: Jonathan at strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk 
> Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547       
>   
>   
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