# $Id: README 577 2006-10-11 16:51:51Z indraneel $

Program: PALSSE (formerly PAL8E, PSSD)
(Predictive Assignment of Linear Secondary Structural Elements
from Protein C-alpha Coordinate Data)

Author: Indraneel Majumdar <indraneel@chop.swmed.edu>

Algorithm developed by:
	Indraneel Majumdar <indraneel@chop.swmed.edu>
	S. Sri Krishna <krishna@chop.swmed.edu>
	Nick Grishin <grishin@chop.swmed.edu>

PALSSE is released according to the terms of the Biopython license.
(http://www.biopython.org/static/LICENSE)

PALSSE has been tested on Debian GNU/Linux testing/unstable on the i386/opteron
hardware.

Further instructions are in the doc/ section of this release.

Quick instructions:

Install python >=2.3 (2.2 may work but is untested)
Install the python modules:
	Numeric
	Scientific
	bz2
	gzip
	math
	types
	time
	traceback
	ConfigParser

Download and install the modified Biopython distribution available with PALSSE.

Install gcc >=3.3.5 (lower versions may work but are untested)

cd src
make

cp ../etc/pal8e.conf ~/.pal8e.conf

python PALSSE.py <input filename with PDB coordinates>

Output file will be located in the current directory with a .ssd
extension after the first 4 characters of the input filename.

Please use and test PALSSE in any way you like. User feedback will be
greatly appreciated.
