It allows the visualization of several molecules with various representations such as lines, space-filling models, balls and sticks, and backbone ribbons. With this program, information on secondary structure can be read from files or can be assigned. Arbitrary 2-dimensional shapes can be extruded to represent secondary structures. Molecular surfaces can be computed and displayed selectively. Many additional commands, such as a driver for ray tracing in POVRay, geometric measuring tools, and flexible coloring and labeling commands, are also available.
Users click buttons to specify how and where to launch the jobs.
Finally, the results of an AutoDock job are visualized via the graphical user interface. The macromolecule, the initial conformation of the ligand molecule, docked conformations of the ligand and isocontours showing the atomic affinity grids used by AutoDock can be viewed in the Molecular Viewer, which provides access to further analytic tools. In addition, the functionality provided by ADT can be used in script mode, which can automate noninteractive application of AutoDock to high-throughput applications. The Python Volume Viewer is our first attempt to integrate real-time volume rendering into our visualization applications. We wrapped the application program interface of the library driving this board, and we began developing a viewer based on our Python components.