To use STAMP, all users must define the environment variable
STAMPDIR, and set it equal to the directory where you have done
the installation. Users must also have STAMPDIR in their path.
The logical thing is to make modifications to one's .cshrc file to
STAMP reads PDB coordinate information and DSSP information in standard format. Thus, you really must have copies of PDB and DSSP output if you wish to make full use of the program (though DSSP is not, strictly required).
You must create files in the STAMP directory for reading by the program that are specific to your system. These files must be in STAMPDIR/pdb.directories. This file contains a description as to where possible PDB files may be found. The format is:
<directory> <prefix> <suffix> [RETURN]
/data/newpdb/pdb/ pdb .ent /data/newpdb/prerelase/ pdb .ent.Z /usr/people/jack/extrapdb/ _ .pdb.gz ./ myprefix .pdb
A four letter code is meant to go between the suffix and prefix.
For example, the file corresponding the PDB code 4mbn might be
found in the file /data/newpdb/pdb/pdb4mbn.ent. A `_' character
in the suffix or prefix field denotes no prefix or suffix. When
a file is to correspond to a four letter code is to be found, STAMP
routines will try each of the specifications in turn, and will use
the first one found. A recent modification (version 4.2) is to look
in each of the `distr' type sub-directories for filenames. Some people
store PDB files in a format, e.g.
Where the two letter sub-directory name corresponds to the second two characters
in the four letter PDB code (i.e. ignoring the leading number). STAMP now
handles these file types. If you just specify the top directory, the program
will explore suitable two-letter sub-directories corresponding to each file it
is looking for.
dssp.directories contains a description as to where possible DSSP files may be found. The format is as for pdb.directories, e.g.
/data/newdssp/ _ .dssp /data/dssp/ _ .dssp
For example, the DSSP file for 4mbn might be found in the file
STAMP now reads compressed files (.Z or .gz suffixes). In order for this to work properly, you must have the programs zcat (.Z) and gunzip (.gz) installed on your system.