diff --git examples/embeddedWJmol.html examples/embeddedWJmol.html
index f482ebe..5276853 100644
--- examples/embeddedWJmol.html
+++ examples/embeddedWJmol.html
@@ -1,302 +1,303 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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 <head>
   <TITLE>Jalview and Jmol</TITLE>
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   <script>
     <!--//--><![CDATA[//><!--
 var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
 //--><!]]>
   </script>
 <script src="javascript/deployJava.js"></script>
 <script src="jmol/Jmol.js"></script>
 <script src="javascript/jquery-1.4.4.min.js"></script>
 <script src="javascript/jquery.timer.js"></script>
 <script src="javascript/jquery.blockUI.js"></script>
 <script src="javascript/jshashtable-2.1.js" language="javascript"></script>
 <!-- <script src="archive-min.js" language="javascript"></script>
 -->
 <script src="javascript/jalview.js" language="javascript"></script>
 <script language="JavaScript">
 // instead of this, we use a custom JmolApplet spec
 // jmolInitialize('jmol');
 jmolInitialize("","JmolApplet-12.2.4.jar");
 function genHref()
 {
  var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
  for(i=0; i<11; i++)
  { href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); 
  }
  window.location=href;
 }
 </script>
 <script>
  var loglevel=1;
  function dbg(lvl,string) {
   if (_console && lvl<=loglevel) {_console.value += string + "\n";}
  }
  var _lastTime=new Date();
  var _path;
  var _datazip;
  var _zip;
  var alignA;
  var alignB;
  var featuresA;
  var featuresB;
  var pairs;
  var atompairs;
  var structdata;
  var jmolview;
  var jvstructassoc;
  var modeltofiles = new Array();
 
  function lJvA() {
   jvfollower = document.getElementById("jvA");
   setConsole(document.getElementById("stdout"));
   
   sep = jvfollower.getSeparator();
   //jvapp.setSeparator(""+jvapp.getSeparator());
   linkJvJmol(jvfollower, "jmolView", modeltofiles);
  };
 
  var _jvA=new Object();
  _jvA.attributes = {
   code : 'jalview.bin.JalviewLite',
   archive : 'jalviewApplet.jar',
   width : '500',
   height : '350',
   mayscript : 'True',
   scriptable: 'True',
   id : 'jvA'
  };
  _jvA.parameters = {
    java_arguments : "-Xmx256m",
   externalstructureviewer : "true",
    oninit : "lJvA",
   automaticScrolling : "true",
 //  <!-- defaultColour : "Strand Propensity", -->
   file : "uniref50_mz.fa",
   
   relaxedidmatch : "true",
   debug : "true",
   wrap : "false",
   // separator : "^",
   showAnnotation : "false",
   embedded : "true",
   showFullId : "false",
   RGB : "F2F2FF",
   linkLabel_1 : "EMBL-EBI Search",
   linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
   ,
   linkLabel_2 : "Uniprot"
   ,
   linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
   APPLICATION_URL : "http://www.jalview.org/services/launchApp",
   PDBfile : "1gaq.txt FER1_MAIZE",
   permissions : "sandbox"
  };
  jmolSetCallback("hoverCallback","_jmolhover");
   jmolSetCallback("pickCallback","_jmolpick");
   modeltofiles+="1gaq.txt";
 </script>
 
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 	    <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
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 <div id="pageWrap">
 
 <div id="sideNav">
   <ul>
       <li ><a href="applets.html">JalviewLite Examples</a></li>
       <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
       <li ><a href="appletParameters.html">Applet Parameters</a></li>
       <li ><a href="embedded.html">Embedded Alignment</a></li>
       <li class="jvlite-nav-small"><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
       <li ><a href="formComplete.html">Access from Javascript</a></li>
       <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
       <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
   </ul>
 </div>
 
 <div id="content" class="content">
 
 
 <!-- boiler plate link to alternate demopage -->
 
 <div style="width: 100%">
 <div style="width:35%; align:left; float:right;">
 <div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
  Examples aren't working ?<br/>Try <a href="u_embeddedWJmol.html">the unsigned applet demos</a>
 </div>
 <div style="margin:8px; padding:10px; align: left;">
 <p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
 </p></div>
 </div>
 </div>
 
 <!-- content template start -->
 <h2>Structure and Alignment</h2>
 <p>This demo shows how JalviewLite and Jmol can be integrated with the JalviewLite javascript library.</p>
 <center>
  <script>
   jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
  </script>
  <script>
   deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
  </script>
 </center>
 <!-- content template end -->
 
 
 
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 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
 <div id="cite">
 <p>
 If you use Jalview in your work, please cite this publication:
 </p>
 <br />
 <p>
 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
 </p>
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