Protein Models

thingiverse

In 1975, I constructed a wire model of carp muscle calcium binding protein using Byron's bender. Later, I discovered that a Thing-O-Matic could make the process easier by utilizing programs like VMD from the University of Illinois. However, I couldn't print the alpha carbon "trace" representation. Subsequently, I found openSCAD, which allowed me to create nice alpha traces with spheres and cylinders. The openSCAD file could also be modified to construct ball and stick models from orthogonal coordinates of small molecules. Input files were obtained from the Protein Data Bank, identified by a 4-letter code (e.g., 5CPV for carp muscle calcium binding protein). Makescad.f is a Fortran program that outputs calls to an openSCAD module, which is then inserted into makealpha.scad and executed. The resulting STL file took over four hours to print, followed by an hour of carefully cutting the model from support material. Smaller proteins are easier to create. Two provided STL files show a neurotoxin from the green mamba (1FAS) and the iron binding protein rubredoxin (5RXN). GNU Fortran installer is easy to use, with two mouse clicks required for installation and compilation of source code. Byron's bender, VMD, Protein Data Bank, and GNU Fortran are mentioned as resources in this process.