Hello all,
I am trying to write a script that will go through each residue in a
dimer interface and determine for each one how close it is to the
partner monomer.
I can interactively plot all the distances within a certain cutoff
using the handy:
distance chosen, residue_selected_on_first_chain,
partner_monomer_selection, cutoff
For atom selections Warren earlier explained how to parse into its
components (using list=[]; iterate
(selection),list.append((resi,resn))). However, the selection
created by the distance command (i.e. "chosen") does not behave the
same way it seems and I haven't been able to iterate over it to get
at the info.
I see from "help distance" that in the API cmd.distance returns the
average, so it suggested that perhaps minimum and maximum or even
each individual value might also be accessible, giving me hope that
the more elegant solution was close at hand and limited more by my
ignorance than the chosen approach.
Otherwise I suppose there's the more brute-force avenue of going
through each residue, selecting atoms from the partner monomer within
a certain distance if any, and then explicitly measuring the distance
to each atom one by one, but I thought I'd check with the community
before launching such an ugly attack on the problem, having walked
that road before!
Also, not to push my luck, but if you'd like to write your
suggestions in both English and Python, my less-than-rudimentary
knowledge of Python will thank you(!)
Cheers and thanks,
Seth
--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Seth F. Harris, PhD
Agard Laboratory
University of California, San Francisco
Mission Bay Genentech Hall
600 16th St. Suite S416
San Francisco, CA 94143-2240
415.502.2930
