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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.
Jmol - Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry...
ACD/ChemSketch - ACD/ChemSketch for personal and academic use brings the power of our structure drawing package to your home computer.
UCSF Chimera - UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular...
BKchem - BKChem is a free (as in free software :o) chemical drawing program.