This is one of the fastest ways to validate a model and its data (presuming that the difference map comes from a post-refinement mFo-DFc map). It highlights regions where the model and the data do not agree.
Lesser peaks within a certain distance (by default, 2.0Å) of a large peak are not shown. This cuts down on the number of times one is navigated to a particular region because of ripple or other noise peaks around a central peak.
This value can be queried:
(difference-map-peaks-max-closeness)
and adjusted:
(set-difference-map-peaks-max-closeness 0.1)