Usage:
shape shape options

The shape command creates a surface model of the specified shape:

• sphere
• cylinder (open-ended)
• icosahedron

Examples:

shape sphere color dodger blue radius 25
shape icosahedron radius 100 ori 2n3 lattice 1,2 sphere 0.2 line 2

radius r
Set sphere, cylinder, or icosahedron radius to r in physical units of length (default 10). For an icosahedron, this is the distance from the center to a 5-fold vertex.

divisions d
Set the fineness of surface triangulation; d is the number of square mesh cells around the circumference (default 72). The number of triangles around the circumference is roughly 2-4 times higher, depending on the shape and on the value of d. This setting does not apply to an icosahedron with lattice specified, as it will be shown with the indicated numbers of hexagons and pentagons rather than with triangles.

color colorname
Set the surface color to colorname, which can be any color name that specifies a single color (default gray).

mesh true|false
Whether to display the surface as a mesh or as a solid surface. The default is false except for an icosahedron with lattice specified.

linewidth width
The width is the pixel linewidth of mesh display (default 1.0).

height h
Set cylinder height to h in physical units of length (default 40).

sphereFactor f
The shape can be an interpolation between an icosahedron and a sphere of equal radius. The sphere factor f is the weight of the sphere component in the interpolation and can range from 0 (default, icosahedron) to 1 (sphere). The interpolation only affects vertex positions and will not generate curved mesh lines or curved surface triangles.

lattice h,k
A shape with icosahedral symmetry (like many virus capsids) can be idealized 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 (details...). Hexagons are bent where they cross from one triangular face to another. The indices h and k can each be zero (but not both zero) or a positive integer. Surface generation can be slow if large values are used. If lattice is not specified, the icosahedron surface will be shown with triangles rather than with hexagons and pentagons.

orientation type
The type of 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