CrystalMaker is a fantastic molecule-drawing program that lets you build 3D molecular structures; structures can be edited, manipulated and visualized according to various parameters... And, best of all, with blue-red glasses, you can see the whole thing in stereo relief.
My knowledge of chemistry is a little dated; it's far surpassed by the possibilities offered by this software, but not to the point of denying the appeal of such a tool within the framework of a chemistry course. It's a great way to put a practical spin on the highly theoretical conceptualization of atomic orbitals, valences and charges.
Tutorials accompany the software, but the whole thing is fairly technical and requires knowledge of both 3D drawing nomenclature and chemistry. Most molecule banks can be linked to it.
With its counterpart, "CrystalDiffract", you have access to high-level tools.
Runs on Mac and Windows. A demo version is available free of charge.
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