Animations of molecular vibrations

One of the key parts of my dissertation was about molecular vibrations. Basically, Raman and Infrared spectroscopic data were/was (yes, were is technically correct but it just doesn’t ever sound ‘right’) showing or not showing a certain vibrational band. The researchers who saw the band all the time said one hypothesis was therefore false. Researchers who sometimes did, and sometimes didn’t see the vibrational band claimed that said hypothesis was in fact, not disproven at all. Sounds obtuse? Well, this was academia.

Anyway, I ran a bunch of quantum calculations using the Orca Quantum Chemistry program suite. First, I optimized the geometry using Density Functional Theory, with a normal mode vibration calculation as well. Then  I utilized more of Orca’s program suite to output frames of the vibrations for molecular visualization programs in a .xyz format. I read these files, then animated vibration using the pymol built from source, (since that allows for more plugins) with the MP4 encoder plugin. (see Pymol_instructions ). An easier, but longer way would have been to tell pymol to output single frame images, then use an external program to turn them into an animation.

So, here they are: selected normal modes of the amino acid, Cysteine, in different protonation states.