Hi Chris
I had something similar recently. The hint I got was to use the script()
function in Jmol.
This seems to do what you need:
(in Jmol script)
var c = script("show chain");
(in _javascript_)
var chains_list = Jmol.evaluateVar( jmolApplet0, 'c');
alert(chains_list);
That can probably be shortened to a single line
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