Currently there is no command to set background transparency. We should add a "set backgroundTransparency true|false" command to do this so you can put it in a script. It will call the setBackgroundOpacity() routine in chimera/printer.py. Until that is added you could use a little Python script transpbg.py:
from chimera import printer
printer.setBackgroundOpacity(True)
and call it from your movie command script with "open transpbg.py"
I have added this command and it will be in tonight's build, except that it is called "set bgTransparency" (instead of "set backgroundTransparency"), similar to "set bgColor".
--Eric
Eric Pettersen
UCSF Computer Graphics Lab