Category Archives: Blender

Visualizing molecular isosurfaces (MOs, etc.) in Blender

For all that I like using Blender as a tool to visualize molecular structures, there are obvious tradeoffs when using general-purpose software instead of something customized for chemistry. One of those tradeoffs is that there’s no obvious way to import various kinds of computational chemistry data.

For me, this is most often molecular orbitals, which we occasionally want to show in manuscripts. So, I started to think a bit about how to render isosurfaces in combination with imported geometries. I briefly considered trying to write something that processes cube files (from Gaussian), but quickly gave up. Instead, I’ve found that Jmol does the job wonderfully, and with minimal fuss.

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An example of a molecular animation in Blender

To me, one of the great advantages of using Blender to visualize molecules is that it’s a unified platform for rendering both high quality stills and animations. Even though I haven’t explored the animation side all that deeply, simple videos of rotating molecules and the like are trivially simple. I use this all the time in my courses to jazz up my lectures as an alternative to yet another bond-line structure.

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A quick intro to importing molecular geometries into Blender through the blmol script

In the last post, I talked about my experiences using Blender to visualize different aspects of my group’s research. In this post, I’ll give a quick introduction to the script I use to import geometries into Blender along with the template I import them into. The script brings in structures in PDB format files and can generate bond-line or space-filling models.

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Space-filling model of a stack of macrocycles, rendered in Blender.

Blender for chemists

Most of the work we do in my group focuses on molecules or systems with somewhat complicated three-dimensional structures. A few years back, I was working on a proposal and found myself spending the better portion of a day struggling to draw a single ChemDraw graphic; it was of a compound with a stacked architecture and I was trying to fudge in a sort of 3D perspective. The process was tedious and the end result was deeply unsatisfying. It started to become clear that the work we were doing really demanded some means of rendering decent images of 3D objects, both molecules and abstract cartoons. That led to a little poking around online and eventually to Blender, a free, open source, professional-grade package for rendering 3D images and animations.

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