The shape command creates a surface model of the specified shape. See also: define, mask, meshmol, ribbon, BILD format
shape sphere center ligand color dodger blue radius 10The shape can be:
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
• shape sphere [ radius r ] general-options
The default radius r is 10.• shape ellipsoid [ radius r | rx,ry,rz ] general-options
The default radius r is 10 along 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 (see coordinateSystem).• shape cone [ radius rbase ] [ height h ] [ topRadius rtop ] [ caps true|false ] general-options
See also: measure inertia
The default radius rbase and height h are 10 and 40, respectively. The topRadius rtop defaults to 0, giving a pointed cone, but values > 0 can be used to produce a truncated cone. The caps option indicates whether to cap the end(s) of the cone or leave them open.• shape cylinder [ radius r ] [ height h ] [ caps true|false ] general-options
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 icosahedron [ radius r ] [ orientation type ] [ sphereFactor f ] [ lattice h,k ] general-options
The radius r is the distance from the center to a 5-fold vertex (default 10). The orientation type can be:• shape rectangle [ width w ] [ height h ] [ widthDivisions dw ] [ heightDivisions dh ] general-options
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.
- 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
See also: hkcage, Icosahedron Surface, Cage Builder
The width w and height h are the X and Y dimensions of the rectangle (both default to 10). The number of surface points in the rectangle along the X dimension will equal 1 + dw and along the Y dimension will equal 1 + dh. Both the widthDivisions dw and heightDivisions dh default to 10, and these settings override the divisions general option.• shape ribbon atom-spec [ width w ] [ yaxis axis ] [ twist t ] [ segmentSubdivisions divisions ] [ bandLength length ] [ followBonds true|false ] general-options*
A ribbon is a smooth path with flat cross-section that connects a series of atoms or markers. The default width w is 1.0. The yaxis axis (default none) and twist t control 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 an axis is given, the ribbon normal is aligned with that axis as closely as possible within the constraints of the path. A constant twist t to be applied at each point along the path can also be specified (default 0°). The axis can be given as:• shape tube atom-spec [ radius r ] [ segmentSubdivisions divisions ] [ bandLength length ] [ followBonds true|false ] general-options*
Coordinate specifications of axis are interpreted in the system of the model containing the first atom in the path. 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 ribbon centered on an atom should be colored to match that atom (default 0.0). The followBonds option 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.
- x - X-axis
- y - Y-axis
- z - Z-axis
- x,y,z (three values separated by commas only) - an arbitrary vector
- an atom-spec of 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 word selected, sel, or picked; any atoms also selected at the time will be ignored.
*The general options center, rotation, qrotation, coordinateSystem, and slab do not apply to ribbon shapes.
See also: ribbon, ribspline, Volume Tracer
A tube is a smooth path with circular cross-section that connects a series of atoms or markers. The default radius r is 1.0. 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 0.0). 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.• shape boxpath atom-spec [ width w ] [ twist t ] [ reportCuts true|false ] [ cutScale s ] general-options*
*The general options center, rotation, qrotation, coordinateSystem, and slab do not apply to tube shapes.
See also: ribbon, ribspline, Volume Tracer
A boxpath is a 3D zigzag of “beam” segments connecting a series of atoms or markers. The beam has a square cross-section of width w (default 1.0), and the twist t (default 0.0°) 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. Setting reportCuts to true gives the locations of such cuts along the four edges of a hypothetical beam; the cutScale s (default 1.0) is a factor for converting these distances from Å to the appropriate physical units.
*The general options center, rotation, qrotation, coordinateSystem, divisions, and slab do not apply to boxpath shapes.
center atom-spec | x,y,z
The center can be set to the center of specified atom(s) or to a point (x,y,z) in the coordinate system specified with coordinateSystem. The default center is (0,0,0).
Rotate the shape angle degrees around the specified axis (ax,ay,az) in the coordinate system specified with coordinateSystem. The default is no rotation.
Apply the rotation specified as a quaternion in the coordinate system specified with coordinateSystem. The default is no rotation.
The coordinate system is indicated by reference model ID number, optionally preceded by #. The coordinate system is used for interpreting the center, rotation, qrotation, and ellipsoid radius arguments. The default is the coordinate system of the new or existing surface model (see modelId).
Set the surface color to colorname, which can be any color name that specifies a single color (default gray).
Name to use for the newly created surface model. If no name is specified, a generic shape name is used (for example, “sphere”).
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.
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.
Whether to display the surface as a mesh or as a solid surface. The default is false except for an icosahedron with lattice specified.
The width is the pixel linewidth of mesh display (default 1.0).
slab width | d1,d2
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).