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.

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

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.

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

---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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