next up previous contents
Next: Multiple alignment using an Up: Worked examples Previous: Worked examples   Contents

Setup of examples

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.


next up previous contents
Next: Multiple alignment using an Up: Worked examples Previous: Worked examples   Contents