In coot I have set the map contour level to 5.0 rmsd and I do Validate -> Difference Map Peaks ...  and the new window shows me where the peaks are...but not all of them. For example, see screenshot attached.

(there are peaks above sg cys80 and sg cy64, both appear in the visual window in coot but only one of them, cys80, in the listing. If I understand clearly, they should both appear in the visual window and in the listing because I have the same filter (5.0 rmsd). Right?