MacMolecule was a simple graphics appliation written by grad students at Arizona State that rendered sprites of different colors and sizes to produce 3D images of molecules. It was fast, ran on both PC (PCMolecule) and Macs (any 680x0 with a math coprocessor or PowerPC). Unfortnatly, it only rendered to screen resolutions so using it to produce figures for journals or posters was impossible.

I wrote a java app to parse the files and convert them to POVRay input files. The java code can also take a series of MacMolecule files, render them with POVRay and then convert them into an animation with FFMpeg.

What I should have done is written a converter from MacMol files to the industry standard PDB format. This would have given this project access to a wide array of other visualization tools.