[phenixbb] difference map peak in coot not showing all peaks?

Paul Emsley pemsley at mrc-lmb.cam.ac.uk
Wed Jun 4 10:01:32 PDT 2014

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.


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