X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FembeddedWJmol.html;h=083e802b71f822de8d3a39603c9693ebee5dc4f2;hb=f54983a4b00eeeba75854bee6d4d2de6a24856e0;hp=a8c803c137a926ffc3a3238c05d66d0f479ba248;hpb=b72f4090d5f4b06bbe6c9bace36bed652a350b82;p=jalview.git

diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index a8c803c..083e802 100644
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -7,7 +7,7 @@
 <meta http-equiv="content-type" content="text/html; charset=UTF-8">
 <meta http-equiv="keywords" content="protein,interaction,domain,alignment,barton group,structure,interface">
 <!-- InstanceBeginEditable name="head" -->
-<script src="http://www.java.com/js/deployJava.js"></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>
@@ -19,7 +19,7 @@
 <script language="JavaScript">
 // instead of this, we use a custom JmolApplet spec
 // jmolInitialize('jmol');
-jmolInitialize("","JmolApplet-12.1.13.jar");
+jmolInitialize("","JmolApplet-12.2.4.jar");
 function genHref()
 {
 	var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
@@ -62,8 +62,8 @@ function genHref()
 	_jvA.attributes = {
 		code : 'jalview.bin.JalviewLite',
 		archive : 'jalviewApplet.jar',
-		width : '100%',
-		height : '35%',
+		width : '500',
+		height : '350',
 		mayscript : 'True',
 		scriptable: 'True',
 		id : 'jvA'
@@ -73,8 +73,8 @@ function genHref()
 		externalstructureviewer : "true",
 	  oninit : "lJvA",
 		automaticScrolling : "true",
-		defaultColour : "Strand Propensity",
-		file : "uniref50.fa",
+//		<!-- defaultColour : "Strand Propensity", -->
+		file : "uniref50_mz.fa",
 		
 		relaxedidmatch : "true",
 		debug : "true",
@@ -219,20 +219,21 @@ pageTracker._trackPageview();
       <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
 <!-- <a onclick="colourStructs();">Colour from jalviews</a>
  -->
+ <center>
     <script>
-   	jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; backbone 0.01; restrict; center *; set selectionhalos true;select 0","jmolView");
+   	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>
 	</td>
 	</tr>
 	</table>
-<form name="console" id="console">
+<!-- <form name="console" id="console">
   <textarea name="output" id="stdout" rows="3" cols="80"
   >Messages  will appear here.</textarea></form>
-	</div>
+	--></div>
 	 <!-- InstanceEndEditable --></td>
     </tr>
   </table>