[Chimera-users] [chimera-dev] Labeling and coloring chains

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 27 15:44:55 PDT 2016


Hi Deniz,
(1) It is easy to specify multiple chains in the command line.  Show the command line from the Favorites menu.  Example 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)

See manpages for color command and for command-line atom-residue-chain specification:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

… and you may want to try a “getting started” tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>
<https://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>

(2) For labeling the chains there are 2 general choices.  
A. For 3D labels that move along with the structure, there aren’t exactly chain labels, but you can choose to label one residue in each chain and then only show the chain ID and not the other residue information.  For example, command “select :10” will select residue 10 in every chain that has a residue 10.  Then you could use menu: Actions… Label… residue… custom, and in that dialog specify you want labels of the form: %(chain)s , Apply.  Disadvantage is that they may be on top of things and hard to see.  Advantage is they move around with the structure and will stay near that residue when you rotate and translate.

B. you can arbitrarily add 2D labels that are just in the XY plane and do not move with the structure, containing whatever text and symbols you want.  In menu, Tools… Depiction… 2D Labels.  Click the Help button on that dialog to see its help.  You can type in each label manually and move it around in the XY plane.  You would want to get the final view for a figure or something close to it, before bothering to add 2D labels. There are examples of 2D labels in these tutorials:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/density.html>

C. Actually there is a 3rd related choice, just putting the mouse over an atom or residue will pop up temporary information that includes its chain ID, and sometimes that will suffice. 

As you can see, there are lots of tutorials and manual pages to explore.  For future reference, chimera-users at cgl.ucsf.edu (CC’d here) is the address for Chimera usage questions.  The chimera-dev list is more for programming-related questions.

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 Apr 27, 2016, at 12:48 PM, Deniz Simsek Buck <simsekd at stanford.edu> wrote:

> Hi,
> I am very new to Chimera. If you have time, I would really appreciate your answers.
> I am working with a structure that contains 80 chains.
> 1. I would like to color 40 chains at once the same color, rather than manually doing it one by one. 
> How do I do this?
> 2. Also, I would like to add labels to the individual chains I choose on the structure.
> How do I do this?
> Thank you,
> Deniz




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