[phenixbb] Refining with NCS

Tom Terwilliger terwilliger at lanl.gov
Mon Aug 25 12:46:33 PDT 2008

Hi Francis,

If you are using autobuild, then it will by default identify the NCS  
and build into a NCS-based density-modified map.  If you build by  
hand, I'd recommend the same map anyhow, because this map has  
automatically adjusted weighting on the NCS, so that regions that do  
not show the NCS should not be averaged (much) and those that do show  
NCS are more NCS-averaged in the density modification procedure.  I  
think if you use the 2Fo-Fc map it will not be adjusted for NCS, but  
rather will show a standard map.  This map may also be useful to  
consult to verify what parts of the structure really are different in  
different NCS copies.

-Tom T

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
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

On Aug 25, 2008, at 1:37 PM, Francis E Reyes wrote:

> Thanks for the reply Pavel
> However, with regard to the NCS maps issue, which should I be building
> to?Does the 2fofoc that phenix puts out adjusted for ncs and use that?
> Thanks
> FR
> On Aug 25, 2008, at 11:59 AM, Pavel Afonine wrote:
>> Hi Francis,
>>> Also if anyone has a paper/protocol for NCS refinement, I'd love to
>>> check it out (to figure out which map to fit to).
>> Just something to keep in mind... I always prefer to run two
>> refinements
>> in parallel with and without using NCS. It's resolution (and
>> data-to-parameters ratio) dependent. I've seen a  number of cases
>> where
>> using the NCS is very beneficial and similar number of cases where
>> it's
>> better to not use NCS (mostly at resolutions ~2-2.5A).
>> I would also check manually the NCS groups that are found by
>> phenix.refine automatically. I have some cases where automatic
>> detection
>> did not yield a good selection.
>> Pavel.
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> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
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