To change an object's transparency value from the default of .3 to a smaller value of .1, one would type the following Tcl script into the console, or write it to a text file and source it (see Using text commands
proc change_transparency {new_alpha} {
# This will always get the correct colors even if VMD
# gains new definitions in the future
set color_start [colorinfo num]
set color_end [expr $color_start * 2]
# Go through the list of colors (by index) and
# change their transp. value
for {set color $color_start} {$color < $color_end} {incr color} {
color change alpha $color $new_alpha
}
}
# to use:
change_transparency .1
You can even make a new popup window to do this:
user add menu Transp
for {set i 0} {$i < 10} {incr i} {
set f [expr $i / 10.0]
user add subitem Transp $f "change_transparency $f"
}