Wattos is a collection of Java programs for structural biology and NMR
spectroscopy. It's programs analyze, annotate, parse, archive, and
experimental NMR data deposited by authors world wide into the PDB and
NMR Restraints Grid
A query interface was developed that provides
longitudinal access to all publicly available NMR restraint data from
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.
Wattos distribution, source, trackers and this home page are all maintained at Google Code.
Can be found here.
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
wattos root installation directory (e.g. /share/Wattos or S:\Wattos for
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
Linux/Mac users follow these steps:
- 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).
'setenv WATTOSROOT wattosroot; source
setenv WATTOSHOME wattoshome If you
use a shell different than tcsh or csh then you will need to modify
- Source this start up shell script
or log out and log back in.
- 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)
- 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).
- Then in the same location you
should define the WATTOSHOME environment variable (e.g.
- 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.
- 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.
- 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
Please cite these references when using Wattos:
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
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
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
- 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
- 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
- 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
- JavaCC authors.
- Ronald Tschalr for the .Z UncompressInputStream class.
- Tim Stevens for the dihedral angle violation algorithm.
- Stephen Ostermiller for the
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
Please contact me
for help, if required.