Step 1. Uncompress and unbundle the distribution using the following command:
zcat pdb-extract-vX.XXX-XXX.tar.gz | tar -xf -
The result of this command is a subdirectory pdb-extract-vX.XXX-XXX in the current directory, which contains the following:
Step 2. Set up the environment variables.
A. Define RCSBROOT environment variable to point to the installation directory.
Assuming that the installation directory is /home/username/pdb-extract-vX.XXX-XXX, execute in the shell:
For C shell users:
setenv RCSBROOT /home/username/pdb-extract-vX.XXX-XXX
For Bourne shell users:
RCSBROOT=/home/username/pdb-extract-vX.XXX-XXX; export RCSBROOT
B. Add "bin" subdirectory to the PATH environment variable.
Assuming the installation directory is /home/username/pdb-extract-vX.XXX-XXX,
For C shell users:
setenv PATH "/home/username/pdb-extract-vX.XXX-XXX/bin:"$PATH
For Bourne shell users:
PATH="/home/username/pdb-extract-vX.XXX-XXX/bin:"$PATH; export PATH
Step 3. Make binary data from ASCII data
Position in the pdb-extract-vX.XXX-XXX/etc directory and run the script binary.sh:
cd pdb-extract-vX.XXX-XXX/etc
./binary.sh
This command will create certain binary data files, using the ASCII data files in data/ascii directory. The resulting files are stored in data/binary directory. Note that it may take several minutes for this step to complete. This step must be executed before the tool can be utilized.