Ribbon diagram

Ribbon diagram

as arrows, and lines or thin tubes for random coils. The direction of the polypeptide chain may be indicated by a colour ramp along the length of the ribbon. [ [http://www.danforthcenter.org/smith/molview/over/overview.html Thomas J. Smith ] ]

Ribbon diagrams are simple, yet powerful, in expressing the visual basics of a molecular structure (twist, fold and unfold). This method has successfully portrayed the overall organization of the protein structure, reflecting its 3-dimensional information, and allowing for better understanding of a complex object by structural biologists.

History

Originally conceived by Jane S. Richardson, her hand-drawn sketches of the ribbon diagrams were the first schematic diagrams to be produced. [Richardson, Jane S. Schematic Drawings of Protein Structures. Methods in Enzymology 115:359-380, 1985.] In 1982, Arthur M. Lesk and coworkers enabled automatic generation of ribbon diagrams through a computational implementation that uses Protein Data Bank files as input. [Arthur M. Lesk, Karl D. Hardman. Computer-Generated Schematic Diagrams of Protein Structures. Science 216:539-540, 1982.] This conceptually simple algorithm fit cubic polynomial B-spline curves to the peptide planes. Most modern graphics systems provide B-splines as a basic drawing primitive. B-Splines are well suited to fitting between data points but not necessarily interpolating through each of those points. To create a line that intersects all data points, Hermite splines work better.

Current computer programs

A popular program used for drawing ribbon diagrams today is Molscript. Molscript utilizes hermite splines to create coordinates for coils, turns, strands and helices. The curve passes through all its control points (Cα atoms) guided by direction vectors. The program was built on the basis of traditional molecular graphics by Jane S. Richardson, Arthur M. Lesk & Karl Hardman, and John Priestle. [ [http://www.avatar.se/molscript/doc/about.html MolScript v2.1: About the program ] ]

Other programs such as PyMOL also produce ribbon diagrams.

Features of ribbon diagrams

References


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