Using the MapColors() proc, I came up with a little proc of my own to easily have transparency with ease in your icons.
proc
transparent(atom/a, l=0.5)
var icon/i = new(a.icon)
i.MapColors(1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,l, 0,0,0,0)
a.icon = i
There ya go, just set l to the amount you would like to use. 1 for 100% opacity, 0 for 0% opacity.