Does anyone know of public-domain programs for making
distance plots ("Ooi plots")? That is, a graphical
representation of an inter-atomic distance matrix?
Ideally, such a program would take as input:
- a PDB file (or other structure format file)
- a specification D of maximum inter-atom distance
(in Angstrom units, for alpha-carbon atoms)
and would output a size N^2/2 plot for a protein of length N,
where a matrix cell i,j is "dark" if and only if the pair (ai,aj) of
alpha-carbons are in proximity ( d(ai,aj) < D ) in the structure.
It wouldn't be a hard program to write. (If I don't find one
I'll probably write one, and make it available. But it would
be nice if I could save some hours/days and grab one off the net).
I scanned the EMBL unix software database, as well as a couple
other repositories on the Web, but didn't see any such programs
listed.
Thanks for any pointers.
-- Evan
Evan W. Steeg steeg at ai.toronto.edu
Dept. of Computer Science steeg at t13.lanl.gov
10 Kings College Circle
University of Toronto Phone: (416) 978-5182
Toronto, Canada M5S 1A4 FAX: (416) 978-1455
