[phenixbb] Generating a list of peak heights in a Bijvoet difference Fourier

Nathaniel Echols nechols at lbl.gov
Fri Mar 23 12:09:39 PDT 2012

On Fri, Mar 23, 2012 at 12:02 PM, John Rose <rose at bcl4.bmb.uga.edu> wrote:
> Is there a way to get a print out of the peak positions and their heights from a Bijvoet difference Fourier map?
> I can generate the map and see the peals but I would like a listing also.

Download the latest nightly build and run this command (or use the GUI):

phenix.find_peaks_holes data.mtz model.pdb

You may also need to specify this to make sure it uses the anomalous data:


(the command is supposed to show options if you run it without
arguments, but I see this is broken - will be fixed next build.)

Among other things, it will produce a list of anomalous peaks above
3sigma (set anom_map_cutoff=X to change this), which will also written
to a PDB file as UNK atoms (chain C).


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