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:
- 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.
- 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)
follow similar
steps:
- 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.
C:\myName\wattoshome).
- 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
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 Start
/ Applet![Applet](applet.gif)
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 Start
/ Applet![Applet](applet.gif)
Under construction.
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
- 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".
Sponsors
Please contact the webmaster
for help, if required.