[responding to Folmer Fredslund, private message]
Thanks, Folmer. What I was missing was the difference between
color colorName, selection
set xxx_color, colorName
set xxx_color, colorName, selection
Each of which does something totally different internally
in PyMOL. I see now that scenes only reproduce the first of these. That
is, they only set the "inherited" color of atoms that we see
specifically when the representation color (dot_color, ribbon_color,
sphere_color, etc, set by the second and third of these commands) is set
That's what was throwing me off.
purposes, it just means that I have to be careful to use only the COLOR
command if I want scenes to reproduce changes in color.
Might be nice to explain that on the wiki. (Or, of course, maybe I missed it there....)