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

A G Szabo agszabo at bell.net
Thu Jan 14 18:27:13 PST 2016


Elaine

Thank you for your prompt reply.

I should probably ask another question going through the generic question email.  But 

In the structure I am working with there is a 25 amino acid segment that is flexible and not represented in the  crystal structure. In the Chimera structure it is represented by a series of dashed lines.  How can I increase the thickness of those branched lines and even change their color from the rest of the protein.

Thank  you

Arthur

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: January-14-16 7:13 PM
To: A G Szabo
Cc: chimera-users at cgl.ucsf.edu
Subject: coloring only specific atoms, or atoms but not ribbon

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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