Protein Models

by pmoews, published

Protein Models by pmoews Oct 8, 2011

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 In 1975 I constructed a wire model, an alpha carbon trace, of carp muscle calcium binding protein using<a href="http://www.umass.edu/microbio/rasmol/history.htm#bender"> Byron's bender</a>.  A Thing-O-Matic, I thought, would allow me to build the same model much more easily.  I began with a program from the University of Illinois, <a href="http://www.ks.uiuc.edu/Research/vmd/">VMD</a>, which displays  protein structures in various ways and outputs STL files.  While I was successful in making models with VMD's "tube" representation I was not able to print the alpha carbon "trace" representation.

 Then I found openSCAD.  All one has to do is provide openSCAD with properly oriented spheres and cylinders and let it work its magic.  It produces nice alpha traces that are very similar to a wire model. As well the openSCAD file provided can be easily modified to construct ball and stick models from the orthogonal coordinates of small molecules.


Input files are obtained from the Protein Data Bank and are identified by a 4 letter code, 5CPV for carp muscle calcium binding protein. Makescad.f is a fortran program that outputs calls to an openSCAD module. Insert the output file into makealpha.scad and execute it. On my machine makealpha.scad took two hours to render and the resulting scaled up STL file a bit over 4 hours to print. Carefully cutting the model from the support material took another hour. The result was the alpha carbon trace of carp muscle calcium binding protein pictured at the above left.

 Smaller proteins are easier to do.  Two provided STL files are a neurotoxin from the green mamba, 1FAS, and the iron binding protein, rubredoxin, 5RXN. The neurotoxin is shown at the left of the bottom image and the iron binding protein on the right.  The N-termini of the proteins are marked in blue and the C-termini in red.

Thousands of sequences are available at the Protein Data Bank and if a smoother model pleases you it is not difficult to clean up the "tube" representation provided by VMD. Note that the current installer for GNU Fortran is very easy to use. Installation requires two mouse clicks. A single command entered at a command prompt compiles the source and produces an executable (gfortran makescad.f -o makescad.exe) A second command with the PDB file available makes the scad calls.
(makescad.exe &lt5CPV.pdb &gt5CPV.out)

Byron's bender www.umass.edu/microbio/rasmol/history.htm#bender
VMD www.ks.uiuc.edu/Research/vmd/
Protein Data Bank www.rcsb.org
GNU Fortran gcc.gnu.org/wiki/GFortranBinariesWindows

updated October 9, 2011 makealpha.scad better smaller stl's

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I have has some success using VMD to make cartoon models, although I sometimes have to repair the STL files using Netfabb.

Thanks for the Fortran source. Any advice on compiling it on linux/mac?

If you can briefly describe how it works I'd love to rewrite it in python...


I've been looking forward to printing this for some time. :)

We have a new UP! printer in the lab which does support material, so I'll try the rubredoxin soon as well.

I just hope I can figure out the Fortran converter to do others.

Nice - I will have to keep this in mind as a teaching resource if I ever do any protein structures

Well done!

I've been interested in doing a ribbon model for a while of proteins, but have been struggling on the way to make models printable by an additive printer like the Makerbot. I'm quite impressed that the tube models you've got turned out so well!

Looking forward to trying that with other models.