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pymol - PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating...
Blender - Blender is the open source, cross platform suite of tools for 3D creation.
BioBlender - BioBlender is a software package built on the open-source 3D modeling software ...
FreeCAD - An open-source parametric 3D modeler
Jmol - Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry...
meshmixer - meshmixer is an experimental 3D modeling tool for making 3D mashups without too much hassle.