[phenixbb] NCS weighting

[Jianghai Zhu]

Hi Tom,

I have similar experiences with the ncs position restraints.  I would  
rather break the ncs to small groups than use loose restraints.   
However, I sometimes found there are big differences between the B  
factors of ncs related groups.  So I tend to use a loose restraints  
on B factors, but that may not be the general case.

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
+++++++++++++++++++++++++++++++



On Mar 27, 2007, at 5:13 PM, 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
>
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