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A colleague here at the University of Pittsburgh recently asked me to give a guest lecture for her graduate class in scientific visualization.

I took the opportunity to point the students to some of the nice work from Mario Valle on errors and mysteries in chemical visualization and standard data and representations. Indeed, preparing the lecture made me think hard about the subject. I first saw molecular visualization tools using OpenGL over 10 years ago. (I also realize that the field dates further.) But almost everyone uses the same ball-and-stick representations.

I’m posting my talk, although you miss a lot without the stories that go along. Put simply, I wanted to discuss what we’re trying to do with the Avogadro project — create a molecular editor and “builder” that works intuitively and fits in a normal workflow. We fully expect that people will use other tools and want to allow interaction and interconversion between them.

Right now, most of the developers come from the small molecule community. So we hope that our project can be extended to work on other problems (e.g., solid state, biomolecules), but have not pushed it hard in those directions.

As I made up the lecture, I really did ask questions about how and why we visualize chemical data — specifically molecules. Can we move beyond balls and sticks?