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
Thanks for any pointers.
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