Interactive Handheld Molecules

A physical ball and stick model of an amino acid is augmented by computer graphics showing the spacefilling model super- imposed. Courtesy of Art Olson, Molecular Graphics Laboratory, The Scripps Research Institute.Thirty years ago, molecular biologists routinely constructed protein models out of brass rods (“Kendrew models”). In recent years, researchers put away such tinker toys and turned to computer graphics.


But now scientists at The Scripps Research Institute are combining the two mediums. They “print” three-dimensional models of biological molecules that, when held and manipulated, interact with the computer that printed them. The work was published in the March issue of Structure.


“Everyone has a gut feeling that there’s something different about holding an object versus looking at it on the screen,” says Art Olson, PhD, professor of molecular biology and director of the Molecular Graphics Laboratory at The Scripps Research Institute. “But because these models are essentially computer output, they have a special relationship to the data in the computer that actually made them.”


Olson and his colleagues generate handheld molecules with 3D fabricating printers that can make solid objects out of layers of plaster or plastic. Then, as a person turns or twists the object, a digital video camera tracks its movements. The computer displays these manipulations as well as additional information about the molecule in what is known as “augmented reality.” For example, as a person moves two physical molecules toward one another, the screen might show how the electrostatic fields and electrical potentials change.


Computer augmentation of two subunits of the SOD dimer which are tracked and manipulated independently. The electrostatic field is shown with small arrows that point along the local field vectors (they appear as small as dots in this picture), and the potential is shown with volume rendered clouds, with positive in blue and negative in red. Courtesy of Art Olson, Molecular Graphics Laboratory, The Scripps Research Institute.Why bother with physical models at all? “If you can print out a custom interface that’s easy to handle and will address whatever problem you’re interested in, then why not try to do that?” Olson says. “You have more tools and more cues if you have the analog physical object.”


Physical models with augmented reality have an advantage over pure computer models because they’re more easily manipulated, Olson says. “It’s easy to tie a knot in a string with your hands. It’s much harder on the screen.” Given a flexible model of a protein, a researcher can pick apart the end terminus and see how it might interact if laid against a different part of itself. “Doing that with a mouse would be relatively difficult.”

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