Sometimes waters can be misplaced - taking the place of sidechains or ligands or crystallization agents such as phosphate for example 1. In such cases the variance of the difference map can be used to identify these problems.
This function is also useful to check anomalous maps. Often waters are placed in density that is really a something else, perhaps a cation, anion, sulphate or a ligand. If such an atom diffracts anomalously this can be identified and corrected.
By default the waters with a map variance greater than 3.5\sigma are listed. One can be more rigorous by using a lower cut-off:
(set-check-waters-by-difference-map-sigma-level 3.0)
The scripting interface is:
(check-waters-by-difference-map imol-coords
imol-diff-map)
where imol-coords is the molecule number of the coordinates that contain the waters to be checked
imol-diff-map is the molecule number of the difference map (it must be a difference map, not an “ordinary” map). This difference map must have been calculated using the waters. So there is no point in doing this check immediately after “Find Waters”. You will need to run Refmac or some other refinement first first 2.