Subject: Re: Protein Spreadsheet

From: "C.F. Matta" <[email-masked]>
Date: Sat, 11 Apr 1998 00:52:17 -0400 (EDT)

Dear Colleagues,

For all of you who expressed interest in the LOTUS123 spreadsheet program
(Peptides Geometry Calculations Spreadsheet PGCS01), the spreadsheet as
well as a draft manual can be downloaded free of charge at the CCL
archives:

   ftp://www.ccl.net/pub/chemistry/data/Protein-spreadsheet
 
The respective names/sizes of the files to do download are:

	pgcs01.wk4                962 KB 
	PGCS_manual.dot           1.1 MB

(Note that the manual is an incomplete, rough first draft, as it is still
in preparation.  It will be announced when completed). 

SUMMARY OF PROGRAM CAPABILITIES:

PGCS 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 backbone dihedrals that 
you may require (not only the usual phi, psi, and omega).
In addition to a properly labeled list of dihedral, you also 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 properly labeled list of hydrogen bond
distances 
and angles along the backbone.  (In this way you can "test" an unknown 
peptide to find its type).
The program can also compute the full distance matrix for peptides that
are smaller than 250 atoms (but can be modified for larger ones up to
8100).
After each calculation, it will automatically provide you with a labeled
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).

I would appreciate any improvements/modifications suggestions or comments.
  
Cheers.

Cherif Matta

Chemistry Department 
McMaster University
1280 Main St. W., Hamilton, Ontario
Canada, L8S 4M1

email:  [email-masked]
Phone: (905)-525-9140 - ext. 22502
Fax:      (905)-522-2509