Protein Database Downloader

by Nik Willmore

Feb 23, 2016

The PDB plug-in was rather inconvenient in requiring your to manually download Protein Database Files and it lacked an atom radius output, so I discovered Python has a built-in http download library, and I added atomic radii from Wikipedia.

The new Cocoon marching cubes plug-in along with Kangaroo MeshMachine to refine the mesh better than the native tweaky Cocoon refine component are included.

The smaller example takes about 15 seconds. The huge one a minute or two.

Just enter the PDB symbol, and you can browse for those here:

http://pdb101.rcsb.org/motm/motm-by-title

The small one above is a DNA repair enzyme wrapped around DNA:

http://www.rcsb.org/pdb/explore.do?structureId=3UGM

Some are just too big to test and will likely blow up Cocoon or at least MeshMachine.

I thought these structures might be useful to 3D printer enthusiasts looking for fun blobby shapes to build with.

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    Mateusz Mazurek

    Hey, where can I download marching cubes components?

    1

    Apr 16, 2016

    • up

      Ryan Hoover

      This looks great, Nick. Thanks for sharing. You may also be interested in the suite of Grasshopper tools called "Alba" that I've just release for synthetic biology. It i

      ncludes a component that allows you to search an amino acid sequence on RCSB, download the best match, and visualize the structure of the protein as a "ribbon" showing beta sheets and alpha helices. You can find more info and download it here. 

      Cheers,

      Ryan

      8

      Apr 18, 2016

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        Nik Willmore

        Lysenin pore:

        http://www.rcsb.org/pdb/explore/explore.do?structureId=5gaq

        Part of a worm toxin. Creates holes in cell membranes.

        Apr 29, 2016