1. To run AbDB pipeline

i) Obtain antibodies.xml from SACs
perl ~/git/abdbCode/bin/getSACsPDBList.pl antibodies.xml >SACS_21April2017

ii) Run script for pipeline
~/git/abdbCode/AbDBpipeline.sh SACS_21April2017

You need to have 2 files in current directory (From where you are calling the script)

1. Text file with list of PDB codes (SACsList.txt)
2. config file (abdb.cfg)

The config file 
1. set abdb_HOME="/acrm/bsmhome/ucbterd/git/abdbCode" or Location of source code.
2. set dataprep_dest="/var/tmp" or where you want to move raw data
3. set webdata_dest="var/tmp/AbDb_WebData" or where you want to move processed data for website