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
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Los Alamos National Laboratory
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