[Chimera-users] opacity for stick representation in chimera
meng at cgl.ucsf.edu
Mon Feb 12 09:47:30 PST 2007
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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