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.
Example
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.
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.
Observations
Web app can't query web servers except the one it came from: "same origin policy" (SOP).
Cross-Origin Resource Sharing (CORS).
Multi-finger touch screen gestures works well for rotation, zooming, translating. Should add Mac touch pad support, get Magic TrackPad for viz vault.
Sculptures over 30 residues need support to maintain shape.
Precision cutting of angles (to within a few degrees) needed to avoid self-intersections.
Tablet webgl is buggy in Chrome Beta (have to touch lower half of canvas), and slow in Firefox.
Good web-page layout requires customization for each device: desktop, 7 inch tablet, smart phone, portrait and lansdscape orientations.
Sloppy PDB parsing in Javascript leads to wrong sculptures. For example, need to take one alternate atoms. How to handle chain breaks?
More to do
Upload your own PDB file.
Clear construction instructions with diagrams, and video demonstration.
Paper templates for cutting metal beams. Use scalable vector graphics (SVG).