[Chimera-users] coloring only specific atoms, or atoms but not ribbon

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 14 16:13:14 PST 2016


Hi Arthur,
If you are coloring your selection with the menu, choose menu: Actions… Color… all options (it’s at the bottom of the menu).  That will open a separate Color Actions dialog, in which you could set the “Color applies to” to “atoms/bonds” to color atoms/bonds only, or “ribbons” to color ribbon segment only, etc. (default is “all of the above”).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/coloractions.html>

If you first display the atoms of the residue, you can Ctrl-click to select a specific atom instead of the whole residue.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html#pickselect>

If you are using the “color" command, you control which types of displays are affected by putting some text right after the color name. 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html>

 For example:

color red,a  sel

…. which colors atoms/bonds only, indicated by the “,a” (no space  before it!!), and instead of selecting and using “sel” you can give residue and atom information directly:

color red,a :55.A at ND1

… to color atom ND1 of residue 55 in chain A, or

color hot pink,r :55.A

… to color ribbon-only (indicated by “,r”) of residue 55 in chain A

The getting-started tutorials include examples of these, but I know it can be hard to find exactly what you want.
<http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>

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 Jan 14, 2016, at 1:59 PM, A G Szabo <agszabo at bell.net> wrote:
> 
> I have to admit that my understanding of the various commands to use for very specific functions in Chimera is difficult for me to find the correct command.
> 
> I know how to color a specific residue using the sequence table and the color chart.
> So how do I color a specific atom in a residue. For example I am interested in coloring the nitrogen of the Asn amide side chain say color red. How can I do this?
> When I highlight a residue and visualize it as a ball and stick, then color it different from the color of the helix, the color of that part of the helix changes to the color of the ball and stick, different from the color of the rest of the helix. 
> 
> How can I reset the color of the helix location of that residue, leaving the ball and stick as another color.
> Thank you
> 
> Arthur Szabo
> Professor Emeritus
> Chemistry and Biochemistry
> Wilfrid Laurier University
> Waterloo Canada.




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