Last week I had found out that getting Adobe 3D via Adobe Acrobat 8/9 would prove relatively difficult for it is an outdated software which is no longer supported by Adobe. Now because of this, when I spoke to Dr. Khuong, I spoke to her about this, and asked what it was she wanted to yield from this project. What she said is that she wanted to replace the Spartan program currently used in the bio lab courses, which is used for 3D molecular viewing, with something that would allow for her students to bring in their laptops to class and would therefore be able to download the files and use them along in class, as well as elsewhere if need be.
From this, having given it a bit more thought, I believe that finding a type of robust software that would be relatively small and easy to install/use, and would have to be cross platform so that everyone in the class would be on the same page. Ultimately, the program I have in mind would result in molecules that would be easily movable, mouse hover would show the name of an individual atom, and would look along the lines of this: