Ok, some suggestions for the popup:

The relevant code is in JmolPopup.htm within function getState()
It says
opener.jmolGetPropertyAsString("stateInfo")

jmolGetPropertyAsString() takes a target applet ID as its 3rd parameter,
http://jmol.sourceforge.net/jslibrary/index.en.html#jmolGetPropertyAsString

so I would

1. set a javascript variable in the mother page which value is set depending 
on your choice ("left" or "right" in your example). Let's say that variable is 
called  whichJmol

2. modify the JmolPopup.htm  source like

function getState(){
        if (theScript) {
                return theScript
        }
        if (!opener) {
          alert("The page that opened this pop-up window is not available.")
          return ""
        }
        var t = opener.whichJmol ? opener.whichJmol : "0";
        return opener.jmolGetPropertyAsString("stateInfo","", t)
}

I think that should do it.


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