2009/7/31 Paul Emsley <[log in to unmask]>:
> Alex Theodossis wrote:
>> Is it is possible to configure the Probe output in Coot not to display
>> contact dots between atoms of the same residue?
> I don't see how to do that in probe, so I guess not. If you can persuade the
> authors/maintainers of probe to create such an option, then Coot will
> support it.
Probe provides a flexible way to define the source and the target
atoms that are used to calculate overlaps.
So if you wish to visualise the environment of a residue with probe
dots, you could specify the residue itself as the source and the rest
of the protein as the target. E.g. for chain A reisude 318:
probe -once -u -stdbonds -mc "chainA 318" "not (chainA 318)"
my-protein-with-H.pdb > my-probe-dots.out
where my-protein-with-H.pdb is the output of reduce. Ultimately one
could build up the whole interaction map residue-by-residue, appending
the new dots onto the already existing ones -- I'd imagine that this
wouldn't be too difficult.
The resulting dots can be read in like this:
(handle-read-draw-probe-dots-unformatted "path/to/the/probe-dots.out" imol 1)
where imol is the reduced model's imol.
But I do agree with Frank that this would be a rather esoteric way of
ps. for those who love to misuse coot in esoteric ways: wait until
coot switches to guile 1.9 (or above) -- that comes with a brainfuck