Wattos Software Package

Content

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 SourceForge.

Documentation

Install Java version 1.4.1 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. 

Web Applications 

The following functionality requires Java 1.4.1 (or higher), either through Web Start or Applet. Please install Web Start and run The SwingSet Demo from that site before attempting the Wattos modules. If the demo fails then follow the documentation on that site for troubleshooting the problem. Send Wattos specific questions directly. Note that you will be asked to trust the application or not. No reporting is done by the application and your data will not be exported to BMRB or other computers by this application. The program files have been signed but the signature has not (yet) been registered with a higher authority. You will, therefore, be reminded that the code is yours to trust or not. By downloading from the BMRB web site you are somewhat guaranteed that the code is actually from the BMRB just like any other program you might have installed.

Sjors  Web StartApplet / AppletApplet
A parser to transform NMR distance, dihedral angle, and RDC restraints from XPLOR/CNS, CYANA, or Discover to NMR-STAR. An example input file (with types: XPLOR/distance/NOE/ambi) can be found here. Parsing the restraints does nothing more than change the file format. I.e. it does not change atom names or link it to the molecular system described in coordinate files. The databases DOCR and FRED have restraints for which these final steps (and more) have been done.

Wattos Web StartApplet / AppletApplet
Under construction.

References

Please cite these references when using Wattos:

Acknowledgments


Thanks for code from:

Sponsors

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