Installation and Usage Notes for the Pdb Extract Application
                            (Binary Distribution)

Note: Binary distribution contains an additional submodule, called PROCHECK,
which does more structure checking. This submodule is not available in
source distribution.


1.  Installation

a.  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:

        bin - subdirectory that contains application executables
        pdb-extract-vX.X - subdirectory that contains several examples in
          its "examples" subdirectory.
        data - subdirectory that contains some data files needed by the
          application. 
        etc - subdirectory that contains utility scripts and application
          software license agreement.
        procheck - subdirectory that contains executables for "procheck"

b.  Set up the environment variables.

    - 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

    - Add "bin" subdirectory to the PATH environment variable.
    Execute in the shell:

        For C shell users:
          setenv PATH "$RCSBROOT/bin:"$PATH

        For Bourne shell users:
          PATH="$RCSBROOT/bin:"$PATH; export PATH

c.  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.


2.  Demonstration

There are several examples included in this distribution. They are located
in the subdirectories of "pdb-extract-vX.X/examples" directory. Each directory
contains the following:

    input_data - contains the input data for the example
    deposit - contains the resulting files:
        Example_x.cif - this is the merged file created by "pdb_extract"
        Example_x_deposit.cif - this is the mmCIF format file for deposit
        Example_x.sf.cif - this is the structure factor for deposit and is
          created by "pdb_extract_sf"
    validation_result - contains all validation results

To execute the examples, position in the appropriate directory and invoke
test.sh and test_script.sh scripts. For example:

    cd pdb-extract-vX.XXX-XXX/pdb-extract-vX.X/examples/Example_1
    ./test.sh
    ./test_script.sh