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ADT, PMV and ViPer are visualization tools developed at the Molecular Graphics Laboratory at the Scripps Research Institute.

AutoDock Tools
The AutoTools suite provides a GUI for setting up and running docking calculations using AutoDock.
An online refernce manual for its various modules is available
ADT also has an online tutorial
Hand out of the 'Using AutoDock with AutoDockTools' tutorial is available
You can also download the sample files for the tutorial [4 MB] in tar.gz format.  On Mac OS X, the StuffIt Expander application will just expand this automatically for you.  Otherwise, at the Terminal, type "gzip -d -c tutorial.tar.gz | tar xvf -" to uncompress the file using the command line.

Python -Based Molecule Viewing environment .
A pdf version of the tutorial is available
Online reference manual is available

Visual Programming Environment
ViPEr is a visual-programming environment in which a user can interactively build networks describing novel combinations of computational methods, and yielding new visualizations of their data without actually writing code.
Online reference manual is available.

MGL Tools are installed on Linux (puffin, emperor, coot and pelican)

To use the tools in the core type:
>setup mgltools &
then type

When publishing using any of the above programs please cite the following:

PMV: Michel F. Sanner. Python: A Programming Language for Software Integration and Development. J. Mol. Graphics Mod., 1999, Vol 17, February. pp57-61.
ViPer: Sanner M.F., Stoffler D. and Olson A.J. (2002). ViPEr, a visual Programming Environment for Python. In Proceedings of the 10th International Python conference. 103-115. February 4-7, 2002. ISBN 1-930792-05-0.

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Last Modified:Wednesday, 14-Jul-2004 10:24:52 EDT by the CSB Staff