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[ubuntu] Simulation Window Considers Black to be Transparent

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http://ubuntuforums.org – I have been using a simulation software called AtomEye (http://li.mit.edu/Archive/Graphics/A/) to visualize some atomic configurations. I have been using it on an old laptop running Ubuntu 10.04 and it has worked fine from the beginning. I installed Ubuntu 12.04 on a newer desktop computer, and it has had transparency issues (see attached images). White is ok, but anything not white is taken as transparent. Atoms can be colored according to relative RGB values, ie 111 = white, 000=black (should be). It turns out, 111 does show up white, but 000 shows up completely transparent and 100 shows (Hardware)