I made these renders using Autodesk Maya2016 (edu license) and Molecular Maya from Clarafi. I am still learning how to use the software, which is incredible powerful and versatile. I have made a ton of weird renders already and these are just a small subset of them.
The main goal is to represent proteins in standard materials just as clay, plastic, glass or metals etc.
Simple molecule rotation videos rendered in Maya and compiled with Photoshop or Virtualdub.