How do I create animations for Pymol:

Place the folder containing all of the enclosed files either at your root login or in some other folder with a defined path from the root login folder.

Open the animation script template file (i.e.  test.pml) with a simple text editor (i.e. TextEdit).  Note the top two lines in the template file.  The first is the path to the directory with all of the files.  The second is the command to execute the script.

I usually will copy the first line of the script, excluding the "#".  For example, in the enclosed template file I would copy "cd ~/TestAnimation/" from the template script and paste it into the box in the upper MacPymol Native GUI next to the PyMOL>  and press return.  If the folder is not at the root directory then revise the path so that MacPymol is looking for the files in the correct directory.

Now copy the second line from the script (i.e copy "@test.pml") and paste it into the same box in the MacPyMOL GUI as before. Press return and viola... you have just executed the script.

If you look at the info in the remainder of the script you will see that the first thing that you execute is a "run movie.py" command.  The file called "movie.py" must be in the same directory as the script and the PDB file and it will be loaded at the time that the script is executed.  All of the movie.py animation commands will now be available.  The rest of the script down to the "viewport 640,480" command line are just a series of Pymol commands that set up the states and initial views of the molecule. 

Below that is the collection of commands that relate to the animation.  They are in two sections.  The first section of commands relate to the actual movements of the molecule. Note the collection of mvSinrot, and mvSinset commands and their syntax.
These commands are followed by the command "movie" to execute the movements.

The second section of the animation commands is for changes in display of the protein using a series of "mappend" commands that will execute the changes at the frames designated by the commands.  Many of the oddball movie commands (i.e. movie.screw) also go here. These commands come after the movie command.

The final section is for ray tracing of the individual frames.  I always have this set of commands commented out (with "#") until I get through troubleshooting the entire animation, because the rendering of each frame can take a LONG time for the animation of a large protein. 

That's it!!

P.S.: I also included a file called "Animation Commands.txt"  that summarizes what the available commands do.  Please note that some of these animation commands do not work correctly, but it is mostly the "wacko" commands that do not work.  The simple commands generally work.  You can test what they do and how the values change the animations by testing them in a script.