From 8e4100988879e992b70e3a810e001671576d5a95 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 21 Jul 2011 16:43:20 +0100
Subject: [PATCH] better layout and structure display on startup

---
 examples/embeddedWJmol.html |   19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index a8c803c..2a3e65a 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>
@@ -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>
-- 
1.7.10.2