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Visualization Of 3D Molecules

By Angela McQuillan

It has been an interesting experience watching Laura Splan integrate herself into the laboratory environment at Integral Molecular. Every day that she is on-site working, she follows a different scientist to learn more about what they are working on. At this point in the residency, she is acting like a sponge for information, gathering all of the resources that are available to her before ultimately deciding on one path to focus on.

As an artist who works closely with data and has written her own software, Laura is attracted to the many different programs that scientists use to visualize their work in the laboratory. This week Laura discovered the PyMOL Molecular Graphics System, which is an open-source program that can create 3D visualizations of proteins and large molecules. Scientists use molecular visualization programs like this to investigate the structure of proteins and nucleic acids, and learn about how they interact with other molecules. This type of visualization is essential to understanding structural biology.

PyMOL is able to visualize and manipulate these molecules, but the molecular information itself comes from the Protein Data Bank. This is a free database for 3D structural data of large biological molecules that are submitted by biologist and biochemists from around the world.

The first thing that Laura did was to perform a search on the PDB for a cotton molecule, since cotton is a material she uses frequently in her artwork.

Cotton molecule found in the Protein Data Bank. Image: Laura Splan

She then uploaded the cotton molecule’s data into PyMOL, and through further manipulation, was able to create this animation:

This was more of a playful experiment by Laura to figure out how to learn to use the software, but images like this can have many different outcomes, including being exported to a 3D printed format.

3D Molecular model in Rhino. Image: Laura Splan