[Chimera-users] changing appearance of dashed lines

Elaine Meng meng at cgl.ucsf.edu
Fri Jan 15 11:06:57 PST 2016


Hi Arthur,
Those dashed lines are “pseudobonds” (like H-bond and distance-measuring lines).  You can Ctrl-click to select one and then click the green magnifying glass icon near the bottom right of the Chimera window to show the Selection Inspector. 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>

In the Selection Inspector, you can Inspect “Pseudobond” and change its color by:
(1) turning “halfbond mode” to “off”, AND
(2) clicking on the square color-well and using the resulting Color Editor dialog to choose a color.  The color will not be visible in the display unless you turn halfbond mode off.

To change line thickness, Inspect “Pseudobond group” (click on the “Pseudobond” and you can see it is a menu where you can change to “Pseudobond group” instead) and then change the “line width” value.

Or, you could do all these things with the “setattr” command
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
…of which there are a few examples in these previous posts:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010614.html>
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010615.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 6:27 PM, A G Szabo <agszabo at bell.net> wrote:

> 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
> 



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