[phenixbb] target omit map

Susan Tsutakawa setsutakawa at lbl.gov
Thu Sep 3 11:28:05 PDT 2009

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.


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