VMD maintains a database of the colors used for the molecules and the other graphical objects in the display window. The database consists of several color categories; each color category contains a list of names, and each name is assigned a color. For example, there is a Resname color category, and within this category there are many names; one for each of the available residue names. Some of these are ALA, CYS, and PRO. Each name can be assigned a color from a list of 17 available colors called the color map. The RGB value of each color can be modified directly in the Color form. Also, each color has a semi-transparent version used when the transparent button is pressed in the Graphics form. To color items in a gradation manner, there are additional 32 colors used in the color scale.
The different color categories in VMD are listed in table 6.1. The Color form can be used to change the assignment of colors to the names in each of these categories. For example, to change the color used to draw Arginine residues when molecules are colored by residue, you would use the Color form, select the `Resname' category, select the `Arg' name there, and then pick the color to use for Arginine's from the list of colors next to the names.
Table 6.1: Color categories used in VMD.