[Chimera-users] changing appearance of dashed lines

Elaine Meng meng at cgl.ucsf.edu
Fri Jan 15 13:12:31 PST 2016

You’re welcome!  I didn’t realize (or forgot if you told me) that you were working on figures for a book… always a big project!  Yes, we would be interested in seeing the results.

On Jan 15, 2016, at 12:37 PM, A G Szabo <agszabo at bell.net> wrote:

> 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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