Is it possible to export a rotating .gif format picture from chemapps.stolaf.edu?
As of now, Java applets only work with Firefox ESR 32-bit. Assuming that OP is using Chrome and Windows 10, in my opinion the best solution would be to use a screen capture software, like ScreenToGif, which is FOSS, has nice interface and is also quite intuitive:



And here is the result:



I must remind though that the major limitation of GIF is that you are stuck with 256 colors. Structures displayed with GIF will never look as slick as those demonstrated in browser with JavaScript.