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 [email protected] 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: [email protected] 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 [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb