Color Secondary Structure colors peptides/proteins by secondary structure: helix, strand, or coil (non-helix, non-strand). Helix and strand assignments are taken from the input structure file or generated with ksdssp. Molecules other than peptides and proteins are not affected.
There are several ways to start Color Secondary Structure, a tool in the Depiction 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.
Checkboxes control which types of secondary structure will be colored, and the colors can be changed using the adjacent color wells.
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.