The only application of this that I know of is producing a movie
for demonstration and having parts of the molecule appear and
disappear slowly. These are very crude scripts and they can be
improved.
# change alpha values for all solid colors.
proc change_alpha {newval} {
set num [colorinfo num]
for {set i 0} {$i < $num} {incr i} {
color change alpha $i $newval
}
}
# vary the alpha value from 0 to 1 thus forcing an object to slowly
# appear on the screen.
proc fade_in {} {
for {set i 0} {$i < 1} {set i [expr $i + 0.05]} {
change_alpha $i
}
}