[Chimera-users] opacity for stick representation in chimera

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 12 09:47:30 PST 2007

Hi Jerome,
First make a transparent color and then use it on the atoms/bonds -  
there are a handful of routes.

You can make the transparent color using the Color Editor (under  
Tools... Utilities; click the Opacity to get a slider for that, then  
adjust the red/green/blue/opacity sliders as desired).  This color  
can be used on atoms/bonds, ribbons, whatever (depending on the  
current target setting under Actions.. Color) by choosing "Actions...  
Color... from editor" or it can be used in coloring commands using  
the color name "fromeditor"

Color Editor description:

Alternatively, you can make the transparent color with the command  
"colordef" and give it whatever name you want.  The new color name  
can then be used in coloring commands.  Color definitions are saved  
in sessions.  Or, if you don't want to save sessions, just make a  
command file with all of your favorite color definitions and read it  
in whenever you want those colors defined.

"colordef" man page:

I hope this makes sense - feel free to write back if it doesn't!
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 11, 2007, at 5:14 PM, Jerome Nilmeier wrote:

> Hi Elaine:
> I was wondering:  can you adjust the opacity of the stick  
> representation in chimera?
> best, J

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