I wouldn't claim it's necessarily the best way, but if I've had decent
luck with scripting the transitions (either pymol or python) to generate
a set of images.  From there, it's fairly easy to encode a movie with
ffmpeg or mencoder.
But it probably depends on the type of movie you're trying to make.

Pete

Thomas S. Leyh, Ph. D. wrote:
> Hello everyone,
> 
>      I'm trying to assess the best way to begin making molecular movies with 
> Pymol.  It seems eMovie is higly rated.  I understand it is a Pymol plug-in, 
> however I gave this a run on my PC (Vista) only to discover, ultimately 
> through Warren, that that approach won't work, a Mac is required.  (This came 
> a surprise since, in in their TRENDS article, the eMovie author's claim that 
> it runs under windows.)  I have access to an iMac (duo 2 core, OS 10.5), and 
> I wonder whether this is the preferred path.  Further, there is the issue of 
> which Pymol version to downloaded.  Finally, is a Pymol build with rigimole 
> required - this is a special (expert) build that requires unix-like, 
> command-line fluency.
> 
>     Thanks a bunch,
> 
> Tom Leyh
>    
> 
> 
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