ADIT WORKSTATION README
Updated: July 23, 2003 

PDB ADIT is a set of application programs for preparing and
checking structure depositions. This is a workstation version 
of the ADIT (AutoDep Input Tool) software similar to that used
at the US PDB deposition site http://deposit.pdb.org/adit/.


INSTALLATION:

Download the compressed tar file appropriate for your platform
(e.g. wwwadit-macosx-version.tar.gz) from:

             http://deposit.pdb.org/software/

Uncompress and unbundle the compressed tar file using the following 
commands, replacing the file name with the name of the file for 
your particular platform.

   zcat wwwadit-xxx-0.xxx-beta.tar.gz | tar -xvf -

Assuming that you have installed the software in the directory 
/home/me the above software creates a directory tree like, 
/home/me/wwwadit-xxx-version.   ADIT requires one top level link 
to locate system components.  If you have installed the software 
in /home/me/wwadit-xxx-version, do the following:

            cd /
            ln -s /home/me/wwwadit-xxx-0.xxx-beta  wwwadit

Creating the above symbolic link may require root permissions on 
your workstation.  

Next create the binary database files used by the adit tools.  Do 
the following:

            setenv RCSBROOT /wwwadit/adit/rcsbapps
            cd $RCSBROOT/bin
            ./binary.csh

Interaction with ADIT components is provided through a web server.
The default configuration will launch an Apache server that can 
be accessed only on the local host.  The web server runs under 
your user and group ids. The web server runs on port 9876.  
Start the ADIT web server using the following commands:

                    cd /wwwadit
                    ./StartAdit.csh

USAGE:

The preconfigured system is set to work on the loopback-interface that
that is provided by default if networking software is installed 
on your workstation.  Once the ADIT web server is started you can
connnect to the system at the following url:

                 http://127.0.0.1:9876/adit/

Instructions for using the ADIT system are part of the on-line
ADIT system.

ADIT includes the PDB validation software suite.   With permission
of the authors, binary versions of the programs PROCHECK, NUCHECK, 
and SFCHECK are also included in this package.

REFERENCES:

PROCHECK: Laskowski, RA, McArthur, MW, Moss, DS, and Thornton,
JM. J. Appl. Cryst., 1993; 265:283-291.

NUCHECK: Feng, Z, Westbrook, J, and Berman, HM. NUCheck. 1998. NDB-407
Rutgers University, New Brunswick, NJ.

SFCHECK - A.A.Vaguine, J.Richelle, S.J.Wodak. SFCHECK: a unified set of 
procedure for evaluating the quality of macromolecular 
structure-factor data and their agreement with atomic model.
Acta Cryst.(1999). D55, 191-205