Chimera Commands Index

hkcage h k options

The hkcage command creates a mesh of hexagons and pentagons to represent the arrangement of proteins in an icosahedral virus capsid. The related tool Icosahedron Surface generates a mesh of triangles rather than hexagons and pentagons. See also: shape icosahedron, meshmol, Cage Builder

The arrangement of subunits in an icosahedral capsid can be described as a sheet of hexagons in which curvature is introduced by replacing certain hexagons with pentagons, as in a geodesic dome. The pentagons occupy the points of the icosahedron, while the indices h and k refer to the number and arrangement of hexagons in each face. A virus T number (T = h2 + hk + k2) is proportional to the number of subunits in the capsid. VIPERdb includes viruses with T = 1, 3, 4, 7, 13, and in a few cases, even higher. For more details, see the VIPERdb description and the following reference:

Quasi-equivalent viruses: a paradigm for protein assemblies. Johnson JE, Speir JA. J Mol Biol. 1997 Jun 27;269(5):665-75.
The required arguments h and k can each be zero (but not both zero) or a positive integer. The calculation can be slow if large values are used.

The mesh is created as a new surface model centered at (0,0,0). Hexagons are bent where they cross from one triangular face of the icosahedron to another, so that certain "hexagon" edges are formed by two straight line segments rather than one.


Option keywords for hkcage can be truncated to unique strings, and their case does not matter. Synonyms for true: True, 1. Synonyms for false: False, 0. A vertical bar "|" designates mutually exclusive options, and default settings are indicated with bold.
radius r
The radius r is the distance from the center of the icosahedron to a 5-fold vertex (default 100.0).
orientation type
The type of icosahedral orientation can be:
color mesh-color
The mesh-color can be any color name that specifies a single color (default white).
linewidth width
The width is the pixel linewidth of the mesh display (default 1.0).
sphere f
The sphere factor f is the weight of the sphere component in an interpolation between an icosahedron and a sphere of equal radius. It ranges from the default of 0.0 (icosahedron) to 1.0 (sphere). The interpolation only involves vertex positions and will not generate curved mesh lines.
replace true|false
Whether to replace an existing hkcage mesh with the new one rather than opening an additional model.