PyMOL

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PyMOL is free software for network analysis and could be interesting, but their business background could cause trouble ("Subscriptions are not required for usage of PyMOL by full-time students or in teaching full-time students. In such cases, however, DeLano Scientific LLC has no obligation to provide ongoing download access, furnish updates, fix bugs, or meet any other needs you may have.").

On the other hand, it's in Debian, so you can apt-get install pymol.

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