Rainbow Rainbow icon

Rainbow uses a range of colors, changing the color per residue, chain, or molecule model. There are several ways to start Rainbow, a tool in the Depiction category. It is also implemented (with more options than the graphical interface) as the command rainbow. See also: Color Secondary Structure, Color Actions

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:

WATER and HET chains are not affected when the color is changed per residue or chain. The coloring cannot be limited to subset of the residues in a chain or a subset of the polymer chains in a model. To assign a unique color to each helix and/or strand in a protein chain, use the rainbow command instead.

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. When coloring per residue or chain, Rainbow sets individual atom colors and per-residue ribbon colors; when coloring per model, it sets model-level colors and removes any atom-level and ribbon color assignments within the models.

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.

UCSF Computer Graphics Laboratory / June 2014