[phenixbb] target omit map

Tom Terwilliger terwilliger at lanl.gov
Thu Sep 3 12:10:06 PDT 2009

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  
by the map you get from the file AutoBuild_run_xx_/OMIT/ 

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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> phenixbb at phenix-online.org
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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

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