BallStick

DESCRIPTION

This module generates a ball and stick representation of a molecule represented in a pyramid. The bonds are represented as cylinders and the atoms as spheres. If the radius is greater than 0.5 then the bonds are not generated.

The optional colormap can be used to color the spheres. If it is omitted, the values used are as follows:

ATOM   NUMBER    COLOR
Hydrogen  1   pale white
Carbon    6   pale green
Nitrogen  7   blue
Oxygen    8   red
Fluorine  9   green
Phosphorus  15    violet
Sulfur    16    yellow
Chlorine  17    green
Bromine 35    gray

INPUTS

Port: Molecule
Type: Pyramid
Constraints: n-layer
Constraints: optional-baseLat
Constraints: n-D compression
Constraints: n-compression type
The source molecule.

Port: Colormap
Type: Lattice
Optional: This port is optional.
Constraints: 1-D
Constraints: 4-vector
A colormap to use to color the atoms. The value from the colormap is the "color" data variable from the chemistry pyramid. The ReadPDB module fills this value with the atomic number of the atom.

WIDGETS

Port: Radius
Type: Dial
Ball radius normalized to Van der Waals radius.

Port: Complexity
Type: Slider
Complexity (or resolution) of spheres and cylinders. 0 is lowest complexity, which results in a crude representation of the geometry that renders quickly; increasing the complexity gives a higher quality representation.

OUTPUTS

Port: Output
Type: Geometry
Sphere and Cylinder geometry.

KNOWN PROBLEMS

SEE ALSO

ReadPDB, Ball, AtomicSurf, Render.
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© The Numerical Algorithms Group Ltd, Oxford UK. 2000