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 = *h*^{2} + *hk* + *k*^{2})
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.The required argumentsJ Mol Biol.1997 Jun 27;269(5):665-75.

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.

radiusr

The radiusris the distance from the center of the icosahedron to a 5-fold vertex (default100.0).

orientationtype

Thetypeof icosahedral orientation can be:

222(default) - with two-fold symmetry axes along the X, Y, and Z axes- 2n5 - with two-fold symmetry along X and 5-fold along Z
- n25 - with two-fold symmetry along Y and 5-fold along Z
- 2n3 - with two-fold symmetry along X and 3-fold along Z
- 222r - same as 222 except rotated 90° about Z
- 2n5r - same as 2n5 except rotated 180° about Y
- n25r - same as n25 except rotated 180° about X
- 2n3r - same as 2n3 except rotated 180° about Y

colormesh-color

Themesh-colorcan be any color name that specifies a single color (defaultwhite).

linewidthwidth

Thewidthis the pixel linewidth of the mesh display (default1.0).

spheref

The sphere factorfis the weight of the sphere component in an interpolation between an icosahedron and a sphere of equal radius. It ranges from the default of0.0(icosahedron) to 1.0 (sphere). The interpolation only involves vertex positions and will not generate curved mesh lines.

replacetrue|false

Whether to replace an existinghkcagemesh with the new one rather than opening an additional model.