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Avogadro
Open source advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers flexible rendering and a powerful plugin architecture.
http://avogadro.openmolecules.net/
Openmolecules.net ~
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MdView
Molecular visualization software specialized for generating animations from molecular dynamics simulations.
http://www.geocities.com/thomas_r_bonner/vis/vis.htm
Geocities.com ~
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