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).