# $CVSHeader: pal8e/doc/README,v 1.2 2005/02/20 00:32:25 indraneel Rel $

Please read the README at the top level of the distribution.

PAL8E runs can be controlled via a configuration file. The
configuration file allows one to specify:

input, output and debug directories
debug level
characters of PDB input file to check for and omit when scanning a directory
filenames to use from a listfile
directory containing listfile
whether postscript plots of sheets are required
whether pymol log files are required
whether insight log files are required
whether to overwrite previous output files
extension for output files
output directories and relative directories for pymol and insight scripts
comparison file input directories for DSSP, stride, sstruc, molauto,
  pross (may be broken)
how many processes to fork (for openmosix cluster or smp machine)
whether to use pvm (for pvm enabled cluster, pypvm required, may be broken)

The configuration file can be specified using the environment variable
PAL8ECONF. If PAL8ECONF is not set a ~/.pal8e.conf file is
required. The provided ../etc/pal8e.conf file is only suitable for
testing. Please change the parameters when you use the program.

Configuration options for pal8e.conf are explained in the
../etc/pal8e.conf example file.

Input files may be compressed (.Z), gzipped (.gz) or bzipped (.bz2).

Installation instructions are provided in the INSTALL file. PAL8E can
currently only be run from the ../src/ directory. A system wide
installation method is not currently available.

To run PAL8E from the ../src/ directory:
cd ../src/
python PAL8E <arguments>

Program can have 0 to 2 arguments:
  No arguments: Multiple file mode, input paths and filenames from
configuration file.
  With arguments: Single file mode. First argument is input filename
with full path. Second argument (optional) is ID to use for output
filenames. First 4 characters of input filename (or complete filename
if filename < 5 charaters) is used as ID if second argument is
missing.
