Subject: Re: CCL:Radial Plots of DNA torsion angles

From: "C.F. Matta" <[email-masked]>
Date: Tue, 7 Apr 1998 19:39:29 -0400 (EDT)

Dear Dr. Hodgson

I think I have exactly what you need.  

I prepared a  LOTUS123 spreadsheet program that could handle polypeptides
of as many as 8100 atoms.
The input is the coordinates in PDB format.  The program then computes
backbone bond angles, distances and ALL sorts of dihedrals that you may
require (not only the usual phi, psi, and omega).  
Along a properly labeled list of dihedral, you get the number of residues
per turn, the height in A of each turn, the delta (twist) angle (twist
between each residue as you look along the axis of the polypeptide, the N
and t parameters. 
In addition, if you input the helix type (e.g. 3-10 helix, pi-helix, etc.)
it will provide you with a list of hydrogen bond distances and angles
along the backbone.
 The program can also compute the full distance matrix for peptides that
are smaller than 250 atoms (but can be modified for larger ons up to
8100).
After each calculation, it will automatically provide you with a labelled
Ramachandran plot as well as averages of all the computed parameters.

All what you need is to input the pdb info and familiarize yourself with
the package.  For the latter purpose, it comes with some test data.

System requirement: any PC with any version of LOTUS123 Version 4 (or
later) running under Windows.

(This program is totally free of charge. I take no responsibility for any
outcome of its use).

Cheers.

Cherif Matta 
Graduate Student
Chemistry Department
McMaster University
Hamilton, Ontario
Canada, L8S 4M1