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Very extensive and detailed manual on instuctables that can guide you trough the process of finding, designing, software needed, exporting and working with 3d printed models of protein molecules.Thanx theabion!
http://www.instructables.com/id/3D-Print-a-Protein-Modeling-a-Molecular-Machine/?ALLSTEPS
Update:
Here is detailed tutorial for Makerbots:
http://am.ascb.org/ascbpost/index.php/compass-points/item/81-3d-print-your-favorite-protein