Source Chem - About

Overview

Hi! My name is Tim Bonzon and I’m a graduate student in structural biology. This site functions as a sort of reverse portfolio, with all the animations and interactions I make licensed as CC0. This means, whether you’re a student or an educator, you are more than welcome to use the interactive demonstrations or the animations in your study, presentations, or anything else! Credit sourcechem.org if you want, although that is not required. The animations were created using a plugin I wrote: https://github.com/kbonzon/Atom-Animator/. It’s a plugin for Blender3D (https://www.blender.org/) and works by generating ready to animate molecule rigs from .cml files generated by ChemDraw.

What is SourceChem?

It’s a simple realization, actually. “A picture is worth a thousand words and an animation is worth a thousand pictures.” Chemistry moves. Atoms and electrons reorient, overlap, attack, tunnel, and experience all sorts of wacky motions. To describe this motion, chemists have used any number of depictions, from dots to arrows. This method, termed “arrow pushing”, is excellent at describing, in detail, chemical reactions.

Figure 1: An actual arrow pushing exercise from one of my organic homeworks. I hope I’ve gotten better since then.

Yet in the end, it’s still a picture, and many chemistry undergraduates have whole galleries of them stashed in their study notes. The idea for SourceChem came from one of those tired undergraduates, me. After drawing the 1000th arrow (for that day), I realized this should be animated. In fact, the very picture suggests it. Moreover, the nuance an animation can convey far exceeds any picture. Therefore, me, as a 3rd year undergraduate, decided to fill the gap between stable images and dynamic animations. After initial attempts and feedback, I set on the ChemDraw-to-Blender3D pipeline. ChemDraw is a tool widely used by chemists for drawing chemical structures. Blender is a free an open source animation software with a broad userbase. I developed (and am developing) a plugin that reads chemical markup files (.cml files) exported from ChemDraw and converts it to a fully rigged molecule in Blender, ready to be animated. With the plugin, an animation went from days to hours to make. I’ve used it several times to spice up a dry thesis/journal-club presentation. Anyways, what is SourceChem? A website. A website home to belief that “a picture is worth a thousand words and an animation is worth a thousand pictures.”