This January, Schrödinger acquired PyMOL after the untimely death of its creator, Dr. Warren DeLano. PyMOL is a sophisticated and widely-adopted open source molecular modeling environment. Prior to the acquisition, Schrödinger worked closely with Dr. DeLano to jointly develop a PyMOL-for-Maestro plugin to allow users of Maestro to export their work to PyMOL.
After importing structures into PyMOL, many researchers go on to render ray-traced images for publication. A lesser-known but nevertheless useful PyMOL feature is the ability to produce high-quality molecular animations. PyMOL can ray-trace each frame in an animation, with saved movies taking on the same high-quality appearance as still images.
Here's one example of a ray-traced animation created with PyMOL (to view the video in full screen, go directly to YouTube).
To create your own animation that transitions between saved scenes in PyMOL, choose Movie > Program > Scene Loop > Steady > 2 seconds each. When PyMOL renders the movie, it will automatically move between your saved scenes, pausing at each scene for two seconds. Tell PyMOL to ray-trace the movie by choosing Movie > Ray trace frames. You can render the movie by choosing one of the output under File > Save movie As.
For more complete instructions on saving PyMOL movies, see the PyMOL community wiki. A complete PDF tutorial with example structures is also available to PyMOL subscribers.