[Chimera-users] Labeling and coloring chains

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 28 10:01:40 PDT 2016


> On Apr 28, 2016, at 8:15 AM, Deniz Simsek Buck <simsekd at stanford.edu> wrote:
> 
> Hi Elaine,
> Thank you for your reply.
> 
> I already changed the chain IDs to different names. I am working with ribosome structure: 44 chains are large subunit and then I want to color them the same color.
> If I already changed chain A to L23, lets say, how do I choose them?
> 
> Also, is there a way to choose different colors than the available ones and also how do I make the label the same color as the chain?
> 
> Thank you very much,
> Deniz
> 

Hi Deniz,
I do not know how you changed the chain names, so it is hard to say.  In PDB format there is only one column allotted to chain ID in the ATOM lines, 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#coords>

...so it can only be one letter or number, as far as I know.  So it would depend on what Chimera thinks are the chain IDs…. for example, it may have only read the single character in column 22 as the chain ID.  You could probably tell by putting the mouse over some atom in the chain and see what information is in the pop-up balloon.

But maybe you used some other format that allows more characters of chain ID.  Nevertheless, it might not be possible to use the range syntax I showed in my previous message (first example included below).  You could try it, but if ranges didn’t work, you’d have to specify all the IDs (again, all of what Chimera thinks are the IDs) in one long command, or in multiple separate coloring commands.

> color red,r  :.A-D
> (meaning: color red ribbons-only in chains A-D in all models)
> 
> color green,a #0:.B,.D
> (meaning: color green atoms-only in chains B and D of model #0)


Instead of changing chain IDs I would recommend using “alias” to give new names to the set of atoms and then use these new names in the coloring commands, e.g.

alias L23 :.X
(meaning assign the name L23 to chain X)
color hot pink,r L23

… of course you could assign the name to a collection of multiple chains if you wanted, e.g.
alias L23 :.X,.Y,.H

You could also use alias with your existing changed chain IDs providing you can figure out what Chimera thinks they are.

As for colors, you can specify an infinite number of colors as RGBs or hexadecimal or first define new color names and use those names, if the built-in set of named colors doesn’t have what you need.  Color specification is described in the same “color” manpage I mentioned before.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html>

Also described in that page are how to specify coloring labels, e.g.
color orange,r,l
(meaning coloring ribbons and labels only)

Again I’ve CC’d the recommended address for chimera questions, chimera-users at cgl.ucsf.edu

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


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