[Chimera-users] changing appearance of dashed lines

A G Szabo agszabo at bell.net
Fri Jan 15 12:37:18 PST 2016


Elaine

Once again you have been very helpful. Thank you very much.  It worked.

I`ll Have to remember to send you a copy of the book when it is completed.

arthur

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: January-15-16 2:07 PM
To: A G Szabo
Cc: chimera-users at cgl.ucsf.edu
Subject: changing appearance of dashed lines

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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