Wattos Software Package

Content

• Description
• NMR Restraints Grid
• Distribution
• Documentation
• Javadoc
• References
• Acknowledgments

Description
Wattos is a collection of Java programs for structural biology and NMR spectroscopy. It's programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.

NMR Restraints Grid
A query interface was developed that provides longitudinal access to all publicly available NMR restraint data from a relational database. This interface is available from the BMRB web site selecting the Restraints bar in the main panel on the right hand side or by clicking here.

Distribution 

Wattos distribution, source, trackers and this home page are all maintained at Google Code.

Javadoc

Can be found here.

Documentation

Install Java version 1.5 or more recent. Download a distribution zip file and unpack it into a system-wide installation directory which will create the wattos root installation directory (e.g. /share/Wattos or S:\Wattos for Windows users) which will be referred to here as WATTOSROOT. All jar files that are required by Wattos have been included. A directory WATTOSHOME can hold your private settings and the last state of the program.

Linux/Mac users follow these steps:

1. Add the following lines to your start up shell scripts (like ~/.cshrc) replacing wattosroot with your location of the wattos root installation directory (e.g. /share/Wattos) and replacing wattoshome with a (new) directory name (e.g. /share/myName/wattoshome).
   alias wsetup 'setenv WATTOSROOT wattosroot; source $WATTOSROOT/scripts/wsetup'
   setenv WATTOSHOME wattoshome If you use a shell different than tcsh or csh then you will need to modify these commands.
2. Source this start up shell script or log out and log back in.
3. Type wsetup and hit return. This will add the required Java code to your Java CLASSPATH so Java will be able to find it.

Windows users (Wattos was initially developed on Windows) follow similar steps:

1. Set the environment variable WATTOSROOT to wattos root installation directory (e.g. S:\Wattos). On Windows XP this can be done by going through Start->My Computer and then right click inside the window in an area without any item. Select Properties from the list. In the System Properties window that pops up select the Advanced tab on the top and then select the Environment Variables button. Create an environment variable WATTOSROOT to point to the wattos root installation directory (e.g. S:\Wattos).
2. Then in the same location you should define the WATTOSHOME environment variable (e.g. C:\myName\wattoshome).
3. Still  in the same location you can find the PATH environment variable which should be appended to include the wattos script  directory (e.g. S:\Wattos\scripts). This last step allows you not to have to type the full path to the installation directory when initializing other settings and starting wattos.
4. Start a shell. On Windows XP this can be done by going through Start->Run and typing cmd in the box and selecting the OK button.
5. In the window that the shell opened type: wsetup.

Then for both OS (Linux and Windows):
To test if the code is working type: wattos and hit return. This should start up the main menu. Wattos will create the home directory (if the environment variable WATTOSHOME was defined and put some settings in there. Type quit (case-insensitive) to stop execution and save the programs current state in the same directory. 

References

Please cite these references when using Wattos:

• Doreleijers J.F., Nederveen A.J., Vranken W., Lin J., Bonvin A.M., Kaptein R., Markley J.L., and Ulrich E.L. BioMagResBank databases DOCR and FRED with converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. J. Biomol. NMR 32, 1-12 (2005). medline 
• Nederveen,A.J., Doreleijers,J.F., Vranken,W., Miller,Z., Spronk,C.A., Nabuurs,S.B., Guntert,P., Livny,M., Markley,J.L., Nilges,M., Ulrich,E.L., Kaptein,R. and Bonvin,A.M. (2005). RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins 59, 662-672. medline
• Nabuurs,S.B., Nederveen,A.J., Vranken,W., Doreleijers,J.F., Bonvin,A.M., Vuister,G.W., Vriend,G. and Spronk,C.A. (2004). DRESS: a database of REfined solution NMR structures. Proteins 55, 483-486. medline
• Doreleijers, J.F., Mading, S., Maziuk, D., Sojourner, K., Yin, L., Zhu, J., Markley, J.L., and Ulrich, E.L., J. Biomol. NMR 26, 139-146 (2003). medline

Acknowledgments

• Eldon Ulrich and John Markley at BMRB for all advise over many years.
• Steve Mading, Dimitri Maziuk, and David Tolmie at BMRB and Zsolt Zolnai for useful discussion on Java implementation techniques.
• Steve Mading for optimizing some SQL queries. 
• Hamid Eghbalnia for suggesting the algorithm to convert ambiguous distance restraint contributions to the most compact form.

Thanks for code from:

• Greg Warren for the PyMol algorithm in modules/chempy/place.py for placing missing atoms.
• Jonathan Brown for the Graph package tira gracefully donated.
• Dimitri Maziuk for letting me rip his SANSJ package.
• David Flanagan for providing the file copy code.
• David Gilbert and Thomas Morgner for the JFreeChart API for plotting graphs.
• Bruno Lowagie and Paulo Soares for the iText library for generating PDF files.
• Folks at CERN for the colt libraries.
• JavaCC authors.
• Ronald Tschalr for the .Z UncompressInputStream class.
• Tim Stevens for the dihedral angle violation algorithm.
• Stephen Ostermiller for the reading/writing API of comma-separated-value files.
• Henrik Bengtsson for doing old-fashioned printf stuff (see here).
• Steven R. Brandt for the XML SAX parser.
• Jack Shirazi for the fast double to String routine from his book "Java Performance Tuning".

Please contact me for help, if required.