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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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We allow them on chem, maybe it didn't get enough attention? – Manishearth Jun 21 '12 at 5:18

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.

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A mod, suggesting a non SE site?! O the travesty. What has this world come to? – amanaP lanaC A nalP A naM A Jun 22 '12 at 17:12
    
That's pretty much the way it should be, isn't it? After all, it's about the best resource, not necessarily the best StackExchange resource. – Pëkka Jul 22 '12 at 17:49

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.

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Mmmyeah, true, but if it's specialized biochemistry knowledge (or whatever the field is called) that he's asking about, it doesn't really feel like a good fit on Superuser. – Pëkka Jul 22 '12 at 18:01

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