[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
>> +++++++++++++++++++++++++++++++
>>
>>
>>
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>>
>
>
>
>
> 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
>
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