The examples described below show how to apply STAMP to particular
problems. A description of the Input and Output and a summary
of all parameters appear in Chapter 4.
All example output files may be found in the directory examples/
within the directory where STAMP is installed. 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 begining you must ensure a few things:
1. That you have set the environment variable STAMPDIR to the name of the
directory containing the various STAMP defaults files. This directory is
called defs/ within the directory where STAMP is installed.
2. Ensure that you have a copy of the PDB, and that you edit the file
STAMPDIR/pdb.directories (see below) to tell the program where the PDB
files might be found (it is OK if they are stored in more than one place,
or with different extensions). Given a PDB code, these programs search
through the various directories until an appropriate file is found.
3. (optional, but worthwhile). Get a copy of DSSP and run it on the PDB
structures used in the examples below (and indeed any others you wish to analyse).
Edit the file STAMPDIR/dssp.directories to tell the program where to find them (in the
same manner as STAMPDIR/pdb.directories). I would recommend putting DSSP files
somewhere central for all users to share (this saves having to run the program many
times on the same PDB files).