better layout and structure display on startup

diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index a8c803c..2a3e65a 100644 (file)
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -7,7 +7,7 @@
 <meta http-equiv="content-type" content="text/html; charset=UTF-8">\r
 <meta http-equiv="keywords" content="protein,interaction,domain,alignment,barton group,structure,interface">\r
 <!-- InstanceBeginEditable name="head" -->\r
-<script src="http://www.java.com/js/deployJava.js"></script>\r
+<script src="javascript/deployJava.js"></script>\r
 <script src="jmol/Jmol.js"></script>\r
 <script src="javascript/jquery-1.4.4.min.js"></script>\r
 <script src="javascript/jquery.timer.js"></script>\r
@@ -62,8 +62,8 @@ function genHref()
        _jvA.attributes = {\r
                code : 'jalview.bin.JalviewLite',\r
                archive : 'jalviewApplet.jar',\r
-               width : '100%',\r
-               height : '35%',\r
+               width : '500',\r
+               height : '350',\r
                mayscript : 'True',\r
                scriptable: 'True',\r
                id : 'jvA'\r
@@ -73,8 +73,8 @@ function genHref()
                externalstructureviewer : "true",\r
          oninit : "lJvA",\r
                automaticScrolling : "true",\r
-               defaultColour : "Strand Propensity",\r
-               file : "uniref50.fa",\r
+//             <!-- defaultColour : "Strand Propensity", -->\r
+               file : "uniref50_mz.fa",\r
                \r
                relaxedidmatch : "true",\r
                debug : "true",\r
@@ -219,20 +219,21 @@ pageTracker._trackPageview();
       <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->\r
 <!-- <a onclick="colourStructs();">Colour from jalviews</a>\r
  -->\r
+ <center>\r
     <script>\r
-       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");\r
+       jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");\r
 </script>\r
   <script>\r
     deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');\r
     </script>\r
-       \r
+       </center>\r
        </td>\r
        </tr>\r
        </table>\r
-<form name="console" id="console">\r
+<!-- <form name="console" id="console">\r
   <textarea name="output" id="stdout" rows="3" cols="80"\r
   >Messages  will appear here.</textarea></form>\r
-       </div>\r
+       --></div>\r
         <!-- InstanceEndEditable --></td>\r
     </tr>\r
   </table>\r