Protein Sculpture Web Application

Tom Goddard
February 4, 2013


Box Beam Sculptures by Julian Voss-Andreae

Sculptures by German sculptor Julian Voss-Andreae,
who lives in Portland, Oregon.

Alpha Helix for Linux Pauling (2004). Made from a 20-foot steel beam, cut into 15 pieces, and rearranged into a 10-foot vertical spiral. Located in front of the home of Linux Pauling, discoverer of the alpha-helix in 1951.

Heart of Steel (Hemoglobin), 2005. The images show the sculpture right after installation, after 10 days, and after several month of exposure to the elements.

Unraveling Collagen, 2005. "Collagen is responsible for skin elasticity, and its degradation leads to wrinkles that accompany aging. I departed from the actual molecular structure and opened up the intertwining helices towards the top which connects the piece metaphorically with aging."

Birth of an Idea, 2007. "Based on the structure of the potassium channel protein. The sculpture was commissioned by Roderick MacKinnon, who won the 2003 Nobel Prize in chemistry "for structural and mechanistic studies of ion channels". Ion channels are of deep significance to us since they form the tiny pores in our nerve cells that let charged atoms go through to ensure that the cells recharge in order to fire repeatedly, which is the process at the basis of all our intellectual and emotional responses to the world and our creative powers."

Light-Harvesting Complex, 2003. "The Light-Harvesting Complex is the smallest unit of the photosynthetic machinery that converts light and water into organic matter and usable energy in plants, thus providing the basis for life on this planet. The sculpture represents the protein scaffolding of the complex and consists of 850 one-inch pieces of wood. It is displayed, like an altar, on the floor of a small empty room with a candle in the center casting shadows of the structures on the wall. The moving shadows are especially fascinating, because they look very much like plants. It is as if the light-harvesting complex originates flora, but with exchanged roles: The macroscopic plants of our world become ephemeral shadows, whereas the microscopic, and ordinarily not perceivable basis for their existence, becomes a tangible object."

Angel of the West, 2008. An antibody installed at the Florida campus of The Scripps Research Institute. Shaped to suggest the Leonardo da Vinci drawing Vitruvian Man.

Sculpture making by students

Dan Gurnon has been having biology and art students make sculptures using Julian's methods and Julian's design software.

Dan is assistant professor of chemistry and biochemistry at DePauw University, a small liberal arts college (2400 students, $500 million endowment) in Indiana. He is interested in molecular visualization, teaching and research, and his name is on 74 Chimera mailing lists messages from 2009 to 2012.

Mark Cut Weld
Weld... Blobs Smooth
Admire Paint Wear

Chimera box beam drawing

Dan Gurnon asked me to add box beam display to Chimera last July. I added command

  shape boxpath <atom-spec>

to create a box beam path through specified atoms.


  open 1ema

  shape boxpath @CA color light green

  ~modeldisp #0

This command can report the distances along the 4 beam edges for cutting a straight beam to make the sculpture segments.

A video from Dan shows how cut segments are assembled.

Another example of box path with 3 chains.

Web application for designing sculptures

At the end of November Dan proposed they would write a Chimera extension to make sculptures to be distriuted to college and high school students.

I told him about our Viral Outbreak
virus viewer Chimera version.

Then realized a web browser application with WebGL would make it much more accessible.

Sculpture app

Building Sculptures - Things that Go Wrong

Tried making 9 small models, 10-30 amino acids / nucleic acids, as Christmas gifts for my family. Used rented miter saw. Took 5 code fixes while making the first model.

Dan Gurnon made a collagen sculpture using the web app while I was on vacation. Web app ignored HETATM records, missed hydroxprolines (every third residue) in collagen. Oops.

Julian Voss-Andreae long ago made a GFP model that did not work because the chain intersected itself. Used his own software. Small errors in cutting cause this problem.

WebGL and web page layout on tablets

WebGL became available in Firefox for Android on tablets and phones in August 2012.

Chrome Beta for Android from January 25, 2013 allows enabling WebGL.


More to do