[Chimera-users] Numbering helices sequentially

[Elaine Meng]

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