Hi Susan, Your SA omit map should have a mean of 0, yes. Note that the SA omit map only has meaning inside the boundaries of the omit region (as illustrated by the map you get from the file AutoBuild_run_xx_/OMIT/ omit_region.mtz). Some things to try: 1. delete the Mg-water cluster from your structure and just refine it with phenix.refine and look at the maps. 2. same as above, but include simulated annealing. This is another way to get an SA-omit map around your Mg-water cluster. If #2 gives a very different result than the phenix.autobuild SA-omit map, then let me know and I will try to figure out why. All the best, Tom T On Sep 3, 2009, at 12:28 PM, Susan Tsutakawa wrote:
I am trying to generate a simulated annealing omit map of a Mg-water cluster in the active site of my protein but when I run the SA omit map, I can only see the Mg when I use the Mgwater cluster as the target pdb.
When I was building the model which did not have the metal present (phases solved by MR), I observed this Mg-water cluster in the Fo-Fc maps. Geometry and distance were ideal, etc. Now that I'm at the final stages of refinement, I would like to do a SA omit map as a figure for the paper. However, if I goto the lowest sigma, I only see the Mg. I'm using coot with the weights included to view the SA omit maps. I noticed that there is very little noise at the lowest sigma and so I'm wondering if the 0 sigma is truly 0 sigma and any suggestions on what to do.
Thank you in advance.
Sincerely, Susan
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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