[Chimera-users] Questions regarding Ribbon Structures

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 5 09:48:24 PST 2018


Hi Alex,
You’re welcome!
Sorry, for interactive display there isn’t an option to “cap” ribbons or sticks where they are clipped.  Only surfaces have that option.

However, there are commands “conic” and “neon” to make static image files in which clipped atoms and backbone tubes (the latter in neon) appear solid inside, as you describe.  It takes more work to use these, because they may use additional parameter files, and because they are static rather than interactive it takes some iteration to get what you want.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/conic.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/neon.html>

If you were to go this route, you probably want “neon” since it can show a tube backbone, somewhat like a fat ribbon.  Conic only shows atomic representations.  However, neon is not available on Windows systems.

To use it, you need a neon.dat file in the working directory.  (Chimera command “cd” sets working directory.)
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/cd.html>

The neon.dat file is just a simple text file with some parameters. It includes explanations, and you can text-edit it to change parameter values like tube thickness and stick thickness.  In Chimera you need to display alpha-carbons to get the tube in the neon results, and also display any other atoms you want shown as sticks.  

For example, with these commands and the attached neon.dat I get the attached image.

open 4hhb
~ribb
disp @ca
rainbow chain
cd ~/Desktop
set bg_color white
clip hither -20
scale 3
neon -f tiff -o test.tiff

To change other things like the lighting in the image you would also need to have a conic configuration file (see conic help linked above), since neon is basically built on top of conic and also uses its parameters.

Sorry it’s not very simple.  I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

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… meanwhile the Chimera window looks like this:

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> On Feb 3, 2018, at 9:29 PM, Alex Yorn <alexyorn at yahoo.com> wrote:
> 
> UCSF Chimera,
> Just discovered your software and it's amazing! Thank you for making it free for academic use! 
> 
> I just have a quick question regarding the possibility of "filling-in" or changing the linewidth of ribbon structures. I would like to have my ribbon structures completely filled in and not hollow, so when I view them with "Side View" opition, I don't see emptiness inside.
> 
> I've attached two photos. The first is a view of the ribbon structure from the outside. The second is a view of the ribbon structure view from the inside, where you can see that it's hollow. I would like to know what function or command to use to correct this so it's complete solid inside. 
> 
> Sincerely,
> Alex Yorn





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