The molprobity tools probe and reduce have been interfaced into Coot (currently, the interface is not as slick as it might be). However, the tools are useful and can be used in the following way:
first we need to tell Coot where to find the relevant executables (typically you would add the following lines to you ~/.coot file):
(define *probe-command* "/path/to/probe/executable")
(define *reduce-command* "/path/to/reduce/executable")
now the probe hydrogens and probe dots can be generated using Validate -> Probe Clashes (or in the Scripting Window):
(probe imol)
where imol is the molecule number of coordinates to be probed. A new molecule with Hydrogens is created (by reduce) and read in.
By default Coot creates a new molecule for the molecule that now has hydrogens. To change this:
(set! reduce-molecule-updates-current #t)
and that, as you can guess, replaces, rather than adds to the “probed” molecule.
This gives a "static" view of the molecule's interactions.
To get a dynamic view (which is currently only enabled on rotating chi angles) add these to your ~/.coot file:
(set-do-probe-dots-on-rotamers-and-chis 1)
To get a semi-static view (dots are regenerated in the region of zone after a "Real Space Refinement"):
(set-do-probe-dots-post-refine 1)