Michael Fogleman

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Ribbon Diagrams February 2017

111 Go 3D Science

Parse PDB files and render ribbon diagrams of proteins.

Ribbon diagrams are 3D schematic representations of protein structure.

You've probably happened upon these before. I always thought they looked very complex and never figured I'd know how to create such a diagram myself. After creating FauxGL, however, I was in search of interesting 3D visualizations and decided to research these interesting diagrams.

Roughly, proteins are chains of amino acids that are pieced together while reading genetic code. As a protein is formed, these chains will fold in various ways, forming helixes, strands, and coils. A ribbon diagram depicts the 3D structure of the protein as well as these common secondary structures.

The Protein Data Bank is an online database of over 130,000 PDB files. These files encode all of the information needed to produce a ribbon diagram. With this software, you can simply type rcsb XXXX where XXXX is the alphanumeric PDB code and a PNG will be generated in a few seconds.