Glad you liked it. Now to ruin it all by suggesting a non-perl solution:)
Have you looked at the power and ease of the (free I believe, but don't quote me), MDL Chime application designed from the ground up for doing exactly this type of thing, and with its own command language.
It runs as a plug-in to either Netscape or IE and runs under Windows or Mac. They also have an older version of the application with a command line interface rather than a GUI interface that runs under Linux. The ouput from this can be used to drive the Chime application from what I understand.
Since writing my original response, I have had a go at doing something along the lines I described and have encountered difficulties with using Tk::Animation myself. Specifically, on my system using my near verbatim copy of a peice of sample code I found kicking around the web, my attempts to load even a simple GIF, a 6k static or a 14k 2 page animation causes Tk to expand to fill all of my available memory (over 200MB!) and then start to swap whilst chewing 100% of my cpu. I have yet to resolve this problem.
In terms of your latest question, I think it would be possible to use multiple layers of GIF's with transparent backgrounds as overlays, and JS buttons and a bit of dynamicHTML or Stylesheet attributes to turn the overlays on and off (show/hide usng visibilty attributes?), but I think that making this run quickly enough to have a reasonable response time as a Server-driven web app would be very difficult indeed. AS I said before, if you just want the protiens to rotate or zoom, that's quite easy, but dragging and dropping on the client with a server driven app would be pushing you luck I think.
Maybe when Perl6 arrives we will see a PerlVirtualMachine plug-in written and it might become viable then, but in the meantime, I think that Java is your way forward as its here now and works.
Now if only there was a Perl to Java Byte-code complier, but I guess thats just too fanciful :^)
I think I would, unless you have extremely good reasons not to, take a long, hard look at MDL Chime, and even if there is some cost involved--I'm sure the plugin is free, but there maybe other components that you would need to purchase. Unless it is hugely expensive, you could probably trade that against the substantial costs of developing such an application in-house.
Good luck, and if your able, keep me informed of your progress, this type of app is a personal favourite of mine.
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