A simplified representation of protein structure which emphasizes the secondary structure elements (SSEs). An alpha helix becomes a circle and a beta strand becomes a triangle - both connected by straight lines. The result is somewhere between a 3D and a 2D picture; spatial proximity is preserved between SSEs along with the chirality of the connections. This latter property is of great importance to topological studies of a protein - this is where the name (Topologically Oriented Protein Structure) comes from.

Chirality information is in the connection of the lines to the elements - attachment to the 'top' of an element (the C-terminus) is indicated by a connection right to the center. The 'base' attachment is shown as a connection to the edge of the circle or triangle. This information is duplicated in the orientation of the triangles (the strand elements) which are either up or down:

          /\         ______
---------/ _\________\__  /         A beta hairpin.
        /    \        \  /---------
        ------         \/
         UP            DOWN

Most cartoons are generated automatically, by a program that uses some sort of simulated annealing. However, not all folds are amenable to this, notably beta propellors which look horrid. These errant rogues have to be hand-finished by a team of goblins. (I guarantee, no-one will still be reading by this point.)

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