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