Chimera Commands Index

shape shape options

The shape command creates a surface model of the specified shape. See also: measure inertia, meshmol, Axes/Planes, BILD format


shape sphere center ligand color dodger blue radius 10
shape cylinder center 12.5,15,15 coord 1 rad 2 caps true
shape icosahedron radius 100 ori 2n3 lattice 1,2 sphere 0.2 line 2
The shape can be: Option keywords and their subkeywords 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.

shape spherecenter atom-spec | x,y,z [ coordinateSystem N ]] [ radius r ] [ slab width | d1,d2 ] general-options

The center can be set to the center of specified atom(s) or to a point (x,y,z) in a specified coordinate system. The coordinate system is indicated by reference model ID number, optionally preceded by #. If coordinates x,y,z are specified but a coordinate system is not, the laboratory frame of reference will be used. The default center is (0,0,0) in the coordinate system of the new or existing surface model (see modelId). The default radius r is 10. The slab option indicates that a shell or slab of finite thickness should be created instead of a single layer of surface. If a single value (width) is supplied, the inner and outer layers of the slab will be offset from the nominal radius r by ±½(width). Alternatively, two values separated by a comma but no spaces can be used to specify the offsets of the two layers independently. Offsets can be positive (outward) or negative (inward).
shape cylindercenter ... ] [ slab width | d1,d2 ] [ radius r ] [ height h ] [ caps true|false ] general-options
The center and slab options are as described above for sphere. The default radius r and height h are 10 and 40, respectively. The caps option indicates whether to cap the cylinder or leave it open-ended.
shape icosahedroncenter ... ] [ slab width | d1,d2 ] [ radius r ] [ orientation type ] [ sphereFactor f ] [ lattice h,k ] general-options
The center and slab options are as described above for sphere. The radius r is the distance from the center to a 5-fold vertex (default 10). The orientation type can be: The sphereFactor option allows generating a shape that is an interpolation between an icosahedron and a sphere of equal radius. The 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. The lattice option allows showing the icosahedron surface with hexagons and pentagons instead of triangles. 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.

See also: hkcage, Icosahedron Surface

shape tube  atom-specradius r ] [ segmentSubdivisions divisions ] [ bandLength length ] [ followBonds  true|false ] general-options
A tube is a smooth path that connects a series of atoms or markers. The default radius r is 1. The segmentSubdivisions setting controls how many straight segments are used to form the curve between a consecutive pair of atoms; higher values give smoother curves. The number of straight segments forming the curve between a pair of atoms will equal divisions + 1 (default 10 + 1 = 11). The bandLength option specifies what length of tube centered on an atom should be colored to match that atom (default 0). The followBonds option indicates whether the tube should follow the directions of the bonds connecting the atoms; the option should be set to false for atoms that are not bonded.

See also: Volume Tracer

General Options

color colorname
Set the surface color to colorname, which can be any color name that specifies a single color (default gray).
modelId N
Open the surface as model number N (an integer, optionally preceded by #). Submodel specifications #N.N (# required) can also be given. The default is the lowest unused number. If a surface model with the same ID number already exists, the new shape is added as another surface piece.
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.
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).