3-D Models made with Chimera

With links to downloadable STL files suitable for printing or import into a CAD package. See also: uPrint tech note, Eduardo's Guide for 3D Printing Proteins, the NIH 3D Print Exchange

4.5S RNA: STL file (15MB)

To create the STL file yourself download this model's PDB coordinates
and then type these commands on the Chimera command line:

open 4.5S.pdb
molmap #0 3 grid 0.3
volume #0 level 0.3 step 1
and finally use Chimera's File -> Export Scene menu and set the File Type to STL.
After you import the STL file into the CatalystEX application supplied with the printer
you have the opportunity to set the scale of the model. The model you see here was
printed using a scale factor of 1.5.
M domain of Ffh protein: STL file (12MB)

4.5S RNA (above) binds to the M domain of Ffh protein to form a ribonucleoprotein
complex, in this case a signal recognition particle. Together with FtsY protein, this
complex is critical to protein transport in both eukaryotes and prokaryotes. It is instructive
to "dock" the flipped base of 4.5S into the binding pocket of Ffh seen here in order to
observe which amino acids residues are important to binding. To learn more about
this important interaction see this published paper from Peter Walter's lab.

Hepatitis B virus: 3-fold symmetry subunits (2.2MB) 5-fold symmetry subunits (0.4MB)

This is a model of only a portion of the virus. The complete model is
still under construction and will be held together with small magnets.

Models prior to dissolving of support material

Nuclear Pore Complex
The density level was not set high enough for this model, causing parts of the protein complex to not be connected.
When the support material was then dissolved, the disconnected pieces fell off.
Rat Liver Vault
Four-piece model design as viewed in Chimera held together with magnets (orange). Design details.
Clathrin Cage: STL file (20 Mb)
Clathrin cage from map EMD 5119 smoothed with 5A Gaussian. Black plastic. 6 inches.
Virus Models
As part of an outreach project to high school science students and teachers, we
printed 150 models of eight different virus structures. These models were handed
out as supplemental material for Prof. Joe DeRisi's 2010 HHMI Holiday Lecture.
Here are the various STL files:
tRNA: STL file (1.5MB)

This is PDB model 4tna shown as ribbon made with Chimera commands

open 4tna
~display
struts @P length 15 loop 80 radius 1.5
export ~/Desktop/4tna.stl
It was printed on a uPrint plus printer in red ABS plastic about 2 inches across.
The "struts" command was added to Chimera August 21, 2013.