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

Theshape 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

**sphere****cylinder****icosahedron****tube**- a tube connecting a series of atoms or markers

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

The•centercan 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 coordinatesx,y,zare 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 (seemodelId). The defaultradiusris10. Theslaboption 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 radiusrby ±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).

The•centerandslaboptions are as described above forsphere. The defaultradiusrandheighthare10and40, respectively. Thecapsoption indicates whether to cap the cylinder or leave it open-ended.

The•centerandslaboptions are as described above forsphere. Theradiusris the distance from the center to a 5-fold vertex (default10). Theorientationtypecan be:The

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
sphereFactoroption allows generating a shape that is an interpolation between an icosahedron and a sphere of equal radius. The factorfis the weight of the sphere component in the interpolation and can range from0(default, icosahedron) to 1 (sphere). The interpolation only affects vertex positions and will not generate curved mesh lines or curved surface triangles. Thelatticeoption 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 indiceshandkrefer to the number and arrangement of hexagons in each face (details...). Hexagons are bent where they cross from one triangular face to another. The indiceshandkcan 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

Atubeis a smooth path that connects a series of atoms or markers. The defaultradiusris1. ThesegmentSubdivisionssetting 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 equaldivisions+ 1 (default10+ 1 = 11). ThebandLengthoption specifies whatlengthof tube centered on an atom should be colored to match that atom (default0). ThefollowBondsoption 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

colorcolorname

Set the surface color tocolorname, which can be any color name that specifies a single color (defaultgray).

modelIdN

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.

divisionsd

Set the fineness of surface triangulation;dis the number of square mesh cells around the circumference (default72). The number of triangles around the circumference is roughly 2-4 times higher, depending on the shape and on the value ofd. This setting does not apply to anicosahedronwithlatticespecified, as it will be shown with the indicated numbers of hexagons and pentagons rather than with triangles.

meshtrue|false

Whether to display the surface as a mesh or as a solid surface. The default isfalseexcept for anicosahedronwithlatticespecified.

linewidthwidth

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