Good, Martin

jmolScript is the regular way to issue commands from the webpage. It 
is equivalent to typing commands at the Jmol script console.

jmolEvaluate is quite advanced (in fact I haven't yet grasped its use 
fully). In general terms, it serves to pass a value from Jmol to 
Javascript.

Please see
http://jmol.sourceforge.net/jslibrary/#jmolScript
http://jmol.sourceforge.net/jslibrary/#jmolEvaluate

I think that basically, with
 jmolEvaluate('select 1.1');
you were doing nothing. The output from evaluate was put nowhere.
This would make sense:
 var x = jmolEvaluate('select 1.1');
in the case that you had to further process the atom expression "x" 
coming from the selected set. That's indeed what you need and you  
are doing for write(), get the result and put it somewhere (the 
textarea to be sumbitted to the server).
But for just applying commands, jmoLScript is the way to go (and its 
relatives, jmolButton, jmolLink etc. which insert GUI controls in the 
page that run the commands when clicked).



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