The installation and configuration of STAMP are explained in Chapter 5. To run the
worked examples you need only install STAMP and set the STAMPDIR environment variable
as described below. It is not necessary to edit the configuration files.
All example output files may be found in the directory examples/
in the STAMP installation directory. There are four sub-directories
in the examples directory corresponding to each of the four protein
structure familes discussed in the examples below (s_prot/, ac_prot/, ig/, globin/).
Before beginning you should set the STAMPDIR environment variable to the name of the
directory containing the various STAMP defaults files. This directory is
called defs/ within the STAMP installation directory. It contains files containing
default parameters and rules for finding PDB and DSSP files. It is not necessary
to edit these files to run the examples. The files are as follows:
1. STAMPDIR/stamp.defaults contains default values for STAMP command line parameters.
Values in this file can be overridden by specifying options on the command line.
2. The file STAMPDIR/pdb.directories file contains a set of patterns which STAMP
uses to find PDB files. This makes it possible for STAMP to use PDB files
located in multiple directories and having various combinations of filename prefixes
and suffixes.
3. STAMPDIR/dssp.directories is similar to pdb.directories but is used by STAMP
to locate files containing secondary structure assignments for PDB structures
generated using the DSSP program.