Rainbow colors molecule models over a range, changing the color per residue, chain, or model. There are several ways to start Rainbow, a tool in the Graphics category.
Individual models or blocks of models can be chosen from the Models list with the left mouse button. Ctrl-click toggles the status of an individual model. To choose a block of models without dragging, click on the first (or last) and then Shift-click on the last (or first) in the desired block.
Options for coloring the chosen molecule models are to Change color every:
The Color range is defined by five color wells, corresponding to starting color, three intermediate interpolation colors, and ending color. The default colors are blue, cyan, green, yellow, and red, in that order. To use a different number of colors (two to four, or more than five) to define the range, use the rainbow command instead.
Apparent color is determined by a hierarchy; briefly, atom colors assigned on a per-atom basis and ribbon colors assigned on a per-residue basis override the model-level color. Rainbow always sets individual atom colors and per-residue ribbon colors; in addition, model-level colors are set when the color is changed per model.
OK performs the coloring and dismisses the dialog, whereas Apply performs the coloring without dismissing the dialog. Defaults restores the color wells to the default colors. Close dismisses the dialog, and Help opens this manual page in a browser window.