[Chimera-users] icosahedral cage

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 17 13:01:47 PDT 2009

Hi Kristin,
My reply mainly echoes Tom's but I'm sending it anyway.  8-)

Although that tool doesn't have a specific control for linewidth, you  
can do it by:

(1) selecting the icosahedron mesh (Ctrl-click on it)

(2) opening the Selection Inspector (click on the greenish button  
near the lower right corner of the Chimera window -- may have a  
magnifying glass on it depending on version -- or, choose "Actions...  
Inspect" from the menu)

(3) in the Selection Inspector, which should be showing "Inspect  
Surface piece" near the top, change the "line thickness" value near  
the bottom

Even though the lines are fatter, they are still flat (not  
"sticks").  If you wanted sticks instead of lines, don't bother with  
the above, and instead use the command "meshmol" to change the mesh  
surface into sticks:

There may be a problem with "meshmol" in the current daily build (I  
just submitted a bugreport) but it works in the production release, 1.3.

The Icosahedron Surface tool generates triangles.  There is a related  
command "hkcage" that shows an icosahedron with pentagons and  
hexagons, and it includes an option for linewidth:

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 17, 2009, at 11:21 AM, Kristin Parent wrote:

> does anyone know if there is a way to increase the line thickness  
> of the
> icosahedron cage in the higher-order structures option? Can't seem to
> figure it out. Thanks in advance. Kristin

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