On 02/06/14 18:13, Murpholino Peligro wrote:

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?

Now...the peaks values are from Phenix doing a Isomorphous Difference Map ... So I do not know if this is from Coot or from Phenix.

Coot doesn't give you (just) a raw list of peaks. It does some distance filtering (i.e. if there is a peak that is close to a previous (higher/deeper) peak, then that lesser peak is not tabulated. I did this so that I didn't get directed again to parts of the map for which I had already fixed the model. And that is the case in this example too, I imagine. If you fix the problem of the big peak, then you will very likely fix the problem for the smaller peak. Paul.