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freebsd-ports/biology/povchem/pkg-descr
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PovChem is a powerful tool to generate a POV format file from a PDB entry.
It supports CPK, Ball-n-Stick and Cylinder model. You could adjust a lot
of parameters to get a good molecuar graphic.
The document could be found at
http://www.chemicalgraphics.com/paul/Manual.html
WWW: http://www.chemicalgraphics.com/paul/PovChem.html