PyMol is a molecule visualization program that can produce nice pretty pictures of biological macromolecules. There seem to be a couple sites that a question regarding this software could go:
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While not on the official Stack Exchange network, BioStar has a good community of people asking and answering bioinformatics questions. I see that others have asked PyMol questions there. At one point, there was a discussion about rolling BioStar into the Bioinformatics Area51 proposal to bring it into Stack Exchange.
I am surprised you didn't consider Superuser. Yes, it's an application used only by a small, specialized audience, but it's an application nonetheless, and that's where application questions go. Even questions like "How do I print from Visual Studio" get routed there, as they're about using an application rather than about programming per se.