Hi George, Well, there is Rainbow (tool or command) but that would color continuously from one end of the chain to another, with each residue a slightly different color. <http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rainbow/rainbow.html> If you want to make helices different colors but with all the residues in the same helix the same color, the procedure would be something like commands: color red helix & :/ssId=1 color orange helix & :/ssId=2 where "ssId" is a residue attribute, the secondary structure identifier. It is necessary to stipulate helix because there might also be a strand 1, strand 2, etc. You could color just ribbons (or just surfaces, or atoms, etc.) with modifiers after the colorname: color goldenrod,r helix & :/ssId=3 This could also be done with menus/dialogs but with more steps that would take a lot more text to explain. Color command documentation: <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/color.html> Colorname list (can also be seen in Actions... Color... all options, Show all colors): <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/colortables.html#allcolors> The process above requires you to pick the colors yourself, in other words, there is currently no "rainbow secondary structure" function. However, if you use the Axes/Planes/Centroids tool to show axes (cylinders) for all helices, each cylinder will be a single color that is the average, or something like that, of the residue colors in that helix. If you had used rainbow before showing axes, each cylinder will be a unique color. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 1, 2011, at 7:15 AM, George Tzotzos wrote:

I've been looking in the archive for a procedure describing the sequential numbering (and differential colouring, if possible) of protein helices to no avail.

I'd appreciate if anyone could suggest a relevant procedure.

Thanks in advance

George