[phenixbb] NCS weighting

Pavel Afonine pafonine at lbl.gov
Wed Mar 28 07:04:15 PDT 2007


Yes, I'm completely agree with Tom.

Pavel.


Tom Terwilliger wrote:
> Hi Jianghai,
>
> Pavel and I have spent a lot of time on this with a systematic study 
> of NCS in refinement, without reaching a final answer, but with some 
> observations. The bottom line:  for most applications tight ncs works 
> pretty well.  It is very difficult to define the best NCS weighting, 
> and there are not that many cases where loose restraints (e.g., 0.5 
> A  of 1.0 A  instead of 0.05 A) do that much good.  It is also not so 
> clear that the NCS restraints are generally making a very positive 
> difference (in free R).
>
> Experiences from yourself and others would be useful to hear!
>
> -Tom T
>
> At 02:38 PM 3/27/2007, Jianghai Zhu wrote:
>   
>> Hi,
>>
>> I am wondering how the NCS weighting in phenix.refine works.  I 
>> guess the default values (coordinate_sigma = 0.05, b_factor_weight = 
>> 10) are pretty tight.  What kind values would be appropriate for 
>> medium and loose NCS?
>>
>> Jianghai
>>
>> +++++++++++++++++++++++++++++++
>> Jianghai Zhu, Ph.D
>> CBR Institute for Biomedical Research
>> Department of Pathology
>> Harvard Medical School
>> 200 Longwood Ave., Boston, MA 02115
>> Ph: 617-278-3211
>> Fx: 618-278-3232
>> +++++++++++++++++++++++++++++++
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>     
>
>
>
>
> Thomas C. Terwilliger
> Mail Stop M888
> Los Alamos National Laboratory
> Los Alamos, NM 87545
>
> Tel:  505-667-0072                 email: terwilliger at LANL.gov
> Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
> PHENIX web site: http:www.phenix-online.org
> ISFI Integrated Center for Structure and Function Innovation web 
> site: http://techcenter.mbi.ucla.edu
> TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>   
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20070328/75a19cbe/attachment-0004.htm>


More information about the phenixbb mailing list