3D Java

My friend and I am developing this program this will draw a 3D model of a molecule. What i want to know is how can i have java show cylinders at different angles. I have the spheres down but i need to know how to do the cylinders. and the other question is how do i color the balls without changing the color of the light?

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You might want to take a look at VTK at http://public.kitware.com/VTK , which has a nice interface into Java, C++ and Tcl. It's free and has done most of the work for you.

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