Movie from scenes
From Pymol build 1.2 onwards , pymol allows you to build movies directly from scenes defined using the "Scene-Append menu item". To do this you will create the scenes combining the views and representations you want and then use the command the command "Movie" - Program - Scene loop - Y rock , then pick a time for which the given scene should rock between camera interpolations .
This assumes that you have freemol installed and configured and available on your path. Failing which you can always save the images and make the movie externally. This very convenient functionality makes movie making a pretty WYSIWYG process.
To quote Warren from a recent pymol newsgroup post
Assuming that you are using the most recent PyMOL 1.2 beta build, first create a Scene for each display you wish to show.
(To do that, show everything the way you want and then select “Append” from the “Scene” menu. Repeat the process for each view / color / representation you wish to show. You can PgUp / PgDown through defined Scenes.)
Then, to create the movie, select “Program -> Scene Loop -> Y-Rock -> # seconds each” from the “Movie” menu.
Now you can write out the movie as either a series of PNG files or an MPEG file using “Save Movie As…” from the “File” menu. Using scenes to create movies is a lot easier than messing around with scripts : )! Cheers, Warren