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).