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Avogadro - Avogadro is a free, fantastically easy to use molecule editor.
ChemDraw - ChemDraw - The Gold Standard for Chemical Structure Drawing and Research Publications.
Gnome Chemistry Utils - The Gnome Chemistry Utils include six chemistry related programs:
XDrawChem - XDrawChem is a free software program for drawing chemical structural formulas, available for Unix...
pymol - PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating...
MolView - Open Source online service