[phenixbb] NCS weighting

Tom Terwilliger terwilliger at lanl.gov
Tue Mar 27 14:13:01 PDT 2007

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:
>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 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

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
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ISFI Integrated Center for Structure and Function Innovation web 
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TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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