Molecule visualization with Blender

So, suppose you have an exotic molecule in some chemistry program, maybe PyMOL or VMD, and it looks hideous in that tiny window. You want to give it a face lift by rendering it in a fancy fashion. You want to show it to your advisor and she will be happy, and let you do everyone else’s visualization work in the future. How do you do that?

The first step is of course to export your molecule to a 3D model. So far I have found that OBJ format is the most reliable. However, PyMOL does not export OBJ with textures, so you will just see a plain white material across the model, but maybe that is what you want.

Then you need to import the model in some 3D animation/rendering package. We will use Blender. It was used to be called Blender3D, when it was just a toy program with ugly UI, but now it has become a full-featured 3D animation package, and its new Cycles renderer is very capable. Usually when you first import the model, it will have some problems. A common one is duplicated vertices. It can be solved by selecting the model, press Tab...