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Materials
VMD allows users to apply a materials property to the
molecular models they create. The material determines such things
as how transparent an object is, or how shiny, or how large the specular
reflections are.
Making objects semi-transparent is a potentially powerful means of
viewing multiple layers of the molecule simultaneously. Imagine a
protein on the surface of, and extending part way into, a membrane.
One way to visualize the extent of the penetration is to represent the
lipids as `Bonds' and make them transparent. That will show the
membrane without completely obstructing the view of the protein.
VMD maintains a database of materials which can be applied to any
representation in the system, much like the database for colors. There
are two default materials, "Opaque" and "Transparent", which cannot be
modified. Each material is defined by five settings, as follows:
material is
- Opacity: a number (0.0 to 1.0) describing the transparency;
1 is solid, 0 is transparent. By default, transparent objects
are drawn with Opacity set to .3
- Ambient: a value describing how strongly the material reflects
ambient light. Ambient light
provides a uniform illumination of objects with a
background lighting of the object color.
- Diffuse: Diffuse reflections are independent of the viewing
direction, but depend on the direction of the light source
with respect to the surface of the displayed object.
- Specular: a number describing the intensity of
specular reflections. Produces highlights, the higher the
value, the smaller and the brighter the highlight.
- Shininess: a number describing how large is the angle of
the specular reflections. The smaller the number the
wider the angle and the more shiny objects appear.
Default corresponds to a Phong exponent of 40.
For details regarding these material properties, consult an elementary
graphics book such as Foley & Van Dam (Computer Graphics).
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