Coloring Molecules and Objects

VMD maintains a database of the colors used for the molecules and other graphical objects which are visible in the display window. It keeps track of

• color name definitions - its RGB value;
• mappings from a color category to color name - so residue name MET is colored yellow
• the current color scale - red to white to blue, and several related parameters

There are 49 colors available in VMD, with color ids ranging from 0 to 48. The first 17 are, in order: blue, red, gray, orange, yellow, tan, silver, green, white, pink, cyan, purple, lime, mauve, ochre, iceblue, and black.

The next group of 32 colors (from 17 to 48) are colors used in the color map, These can be set to one of several ranges with the Color form or the color text command: red$\rightarrow$green$\rightarrow$blue, red$\rightarrow$white$\rightarrow$blue, or black$\rightarrow$white, etc. There are no names for the specific colors. The color map will be discussed in more detail in a section to follow.