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:

• Ambient: The ambient coefficient describes how strongly the material reflects ambient light. Ambient light provides a uniform illumination of objects with a background lighting of the object color. The ambient light factor is generally used to moderate the effects of shadows from direct lighting, making shadows less dark than they otherwise would be.
• 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: The specular coefficient describes the intensity of specular highlights. The higher the specular value, the brighter the resulting highlights.
• Shininess: The shininess coefficient describes the breadth of the angle of specular reflection. The smaller the number the broader the angle and the rougher objects appear. The larger the value of shininess, the narrower the angle of specular reflection, and the smoother the surface. Default corresponds to a Phong exponent of 40.
• Mirror: The mirror coefficient describes the mirror reflectivity of a surface. When the scene is rendered using ray tracing, surfaces with mirror reflectivity will show reflections much like a mirror-polished metal surface.
• Opacity: The opacity coefficient describes how opaque the surface is; 1 is solid, 0 is transparent. By default, transparent objects are drawn with Opacity set to 0.3.
• Outline: The outline coefficient controls shading of sillhouette edges, darkening the visible edges of surfaces where they are nearly perpendicular to the camera view direction. The outline parameter scales the degree of edge shading (darkening).
• OutlineWidth: The outlinewidth coefficient controls the angular width of nearly perpendicular sillhouette edge that is shaded.

For details regarding these material properties, consult an elementary graphics book such as Foley & Van Dam (Computer Graphics).