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
ISFI Integrated Center for Structure and Function Innovation web
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