TrueChem
ImageJ
Gnome Chemistry Utils
ACD/ChemSketch
ChemDoodle
Avogadro
MedChem Designer
MolView
OnePatch
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TrueChem
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ImageJ - and Other Health Care
Gnome Chemistry Utils - The Gnome Chemistry Utils include six chemistry related programs:
ACD/ChemSketch - ACD/ChemSketch for personal and academic use brings the power of our structure drawing package to your home computer.
ChemDoodle - Chemical drawing and publishing software for desktop, web and mobile. Affordable and used by thousands of scientists around the world. Free trial available for immediate download.
Avogadro - Avogadro is a free, fantastically easy to use molecule editor.
MedChem Designer - Free chemical structure drawing program for Windows. Will also run in Linux using WINE.