[Chimera-users] how to color ranges of residues?

[Elaine Meng]

Hi Peter,
There are several examples of command-line specification of models, chains, residues, atoms at the end the Quick Reference (2-page PDF):
<http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/quickref.pdf>

...and the full explanation is in the "atom specification" page of the manual:
<http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html>

For example, you could use commands like:

alias group2 #0:29-34.L,50-57.L,90-95C.L
color lime green,r group2

Actually it could be done in one command without aliasing, but I personally like to do the aliasing because it makes it easier to try different colors without typing all the residue numbers again.  The ",r" after the color name is an example of using the command to color ribbons only (not atoms/bonds, surface patches, etc.). If you omit that, it will color all the representations of those residues. See the "color" manual page:
<http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/color.html>

Commands are really the best for this kind of thing.  However, it could also be done via GUIs only.  You could use Sequence (under Favorites) to select stretches of residues in the sequence view with the mouse, then use the Color Actions dialog, menu: Actions... Color... all options...).

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 Jul 18, 2012, at 5:51 AM, Peter Hornbeck wrote:

> Hi All,
> I am a new user of Chimera and need to quickly prepare an image in which the hypervariable regions of IgH and IgH are colored differently from the constant regions. 
> 
> For example I want to color these ranges in the two IgG chains:
> 
> H chain:      blue: 25-30,  51-59, 97-101
> L chain:      green: 29-34, 50-57, 93 - 95C
> 
> I would greatly appreciate some help in learning how to do this.
> Thanks, Peter Hornbeck
>  list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users