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: [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.
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