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: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortool.html 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: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/colordef.html I hope this makes sense - feel free to write back if it doesn't! Best, E ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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