by pmoews, published
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.
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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...
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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 <5CPV.pdb >5CPV.out)
Byron's bender umass.edu/microbio/rasmol/history.htm#bender
Protein Data Bank rcsb.org
GNU Fortran gcc.gnu.org/wiki/GFortranBinariesWindows
updated October 9, 2011 makealpha.scad better smaller stl's
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