The **shape** command creates a
surface model
of the specified shape.
See also:
**define**,
**mask**,
**meshmol**,
**ribbon**,
**sop**,
geometric objects

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****ellipsoid****cone****cylinder****icosahedron****rectangle****ribbon**- a ribbon connecting a series of atoms or markers**tube**- a tube connecting a series of atoms or markers**boxpath**- zigzag “beams” connecting a series of atoms or markers

•
**shape sphere**
[ **radius** *r* ]
*general-options*

The default•radiusris10.

The default•radiusris10along each axis. If a single value is specified, the result is a sphere. Specifying three values (rx,ry,rz) sets ellipsoid radii along the X, Y, and Z axes, respectively (seecoordinateSystem).See also:

measure inertia

The default•radiusrbaseandheighthare10and40, respectively. The default orientation is with the axis of symmetry (heightdimension) along the Z axis and top towards +Z (seecoordinateSystem). ThetopRadiusrtopdefaults to0, giving a pointed cone, but values > 0 can be used to produce a truncated cone. Thecapsoption indicates whether to cap the end(s) of the cone or leave them open.

The default•radiusrandheighthare10and40, respectively. The default orientation is with the axis of symmetry (heightdimension) along the Z axis (seecoordinateSystem). Thecapsoption indicates whether to cap the cylinder or leave it open-ended.

The•radiusris 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,Cage Builder

The•widthwandheighthare the X and Y dimensions of the rectangle (both default to10). The number of surface points in the rectangle along the X dimension will equal 1 +dwand along the Y dimension will equal 1 +dh. Both thewidthDivisionsdwandheightDivisionsdhdefault to10, and these settings override thedivisionsgeneral option.

A•ribbonis a smooth path with flat cross-section that connects a series of atoms or markers. The defaultwidthwis1.0. Theyaxisaxis(default none) andtwisttcontrol ribbon orientation and how it varies along the path. If neither is specified, the ribbon normal varies along the path so that there is no local twist. If anaxisis given, the ribbon normal is aligned with that axis as closely as possible within the constraints of the path. A constanttwisttto be applied at each point along the path can also be specified (default0°). Theaxiscan be given as:Coordinate specifications of

x- X-axisy- Y-axisz- Z-axisx,y,z(three values separated by commas only) - an arbitrary vector- an
atom-specof exactly two atoms (not necessarily bonded or in the same model) or one bond. A bond can only be specified by selecting it and using the wordselected,sel, orpicked; any atoms also selected at the time will be ignored.axisare interpreted in the system of the model containing the first atom in the path. 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 ribbon centered on an atom should be colored to match that atom (default0.0). ThefollowBondsoption indicates whether the ribbon should follow the directions of the bonds connecting the atoms; the option should be set to false for atoms that are not bonded.

^{*}The general optionscenter,rotation,qrotation,coordinateSystem, andslabdo not apply toribbonshapes.See also:

ribbon,ribspline,Volume Tracer

A•tubeis a smooth path with circular cross-section that connects a series of atoms or markers. The defaultradiusris1.0. 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 (default0.0). 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.

^{*}The general optionscenter,rotation,qrotation,coordinateSystem, andslabdo not apply totubeshapes.See also:

ribbon,ribspline,Volume Tracer

Aboxpathis a 3D zigzag of “beam” segments connecting a series of atoms or markers. The beam has a square cross-section ofwidthw(default1.0), and thetwistt(default0.0°) sets the rotational orientation of the segments about their long axes. To make a physical replica of the boxpath (see the sculpture at DePauw), the segments could be generated by angled cuts along a single straight beam. SettingreportCutstotruegives the locations of such cuts along the four edges of a hypothetical beam; thecutScales(default1.0) is a factor for converting these distances from Å to the appropriate physical units.

^{*}The general optionscenter,rotation,qrotation,coordinateSystem,divisions, andslabdo not apply toboxpathshapes.See also: Box-Beam Protein Sculpture Design

centeratom-spec|x,y,z

Thecentercan be set to the center of specified atom(s) or to a point (x,y,z) in the coordinate system specified withcoordinateSystem. The default center is (0,0,0).

rotationax,ay,az,angle

Rotate the shapeangledegrees around the specified axis (ax,ay,az) in the coordinate system specified withcoordinateSystem. The default is no rotation.

qrotationqx,qy,qz,qw

Apply the rotation specified as a quaternion in the coordinate system specified withcoordinateSystem. The default is no rotation.

coordinateSystemN

The coordinate system is indicated by reference model ID number, optionally preceded by #. The coordinate system is used for interpreting thecenter,rotation,qrotation, andellipsoid radiusarguments. The default is the coordinate system of the new or existing surface model (seemodelId).

colorcolorname

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

modelNamename

Name to use for the newly created surface model. If no name is specified, a generic shape name is used (for example, “sphere”).

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).

slabwidth|d1,d2

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).