On Jun 1, 2009, at 5:03 PM, Thomas Goddard wrote:

  There are two ways to go about this.  One is to use the color command

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/color.html

say 20 times in a script to gradually increase the transparency to 1. 
You can specify the color as 4 values r,g,b,a in Chimera 1.4 daily 
builds (but not in 1.3). 

A similar approach that does work in the 1.3 release is to color your ribbons with a color you defined with the 'colordef' command. You can then keep redefining the color to change its transparency and the ribbons will change accordingly.

--Eric