2nd try

It seems that the popup page cannot read variables from the opener page 
(at least in my Firefox Win), so I've changed the procedure:

 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. change the newAppletWindow() function in new.js to read and use that 
variable in the link, like

 var newwin=open("JmolPopup.htm?whichJmol=" + whichJmol,"jmol_"+sm, 
woptions2)

Note I am using the same word for the variable name and the URL 
parameter; they could be different.

 3. 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 = location.search.split('whichJmol=')[1];  //this is crude, may be done 
safer
 return opener.jmolGetPropertyAsString("stateInfo","", t ? t : "0")
 }


Ah, everything is fine here.


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