Thank you for your responses!  The fog was indeed the problem.

A contributer to wikipedia was kind enough to share his code for generating
some images of molecular models, e.g.:

http://en.wikipedia.org/wiki/Image:7TM4.png
http://en.wikipedia.org/wiki/Image:GPCR_mechanism.png

The fog is necessary to create the nice 3D depth effect.  I suppose there is
no way to replicate this effect and also maintain transparency?

Thanks,
Shawn

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