Rendering with Fresnel

It's convenient to have a nice rendering tool for molecular systems. ChimeraX is the best GUI option hands down, but sometimes a scripted option is better because it's shareable, repeatable and often more customisable. The Fresnel library is a great option for python.

This is a short post just to show how Fresnel works (see Gist below). I wrote this example code a couple of years ago, and tested it yesterday - it's still current. One nice thing about rendering proteins from scratch is that it really forces you to realise that the core of computational med-chemistry is just a bunch of 3 x n_atoms arrays, to represent the xyz coordinates, and n_atoms x n_atoms arrays for the bonding/adjacency matrix. Realising this takes one from using tools towards writing tools.