IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

Protein Structure Distance Plots?

Evan W. Steeg steeg at cs.toronto.edu
Sun May 14 15:22:24 EST 1995

  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

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

More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net