X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2FhelpTOC.xml;h=59d30e4db4122dd5b287e490eec361c0737eadee;hb=649c3dff0ddf4047b11e83950642501897c60d5c;hp=fc523480f7449d6db24a5467fc6a47705ddea4b1;hpb=8c5dab7c7f049ac9f65a096bb243895cc49e4cd4;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index fc52348..59d30e4 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -2,15 +2,17 @@
 <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
-	<tocitem text="What's new" target="new" expand="true"/>
-        <tocitem text="Release History" target="release"/>
-        <tocitem text="Editing Alignments" target ="edit"/>	
-        <tocitem text="Cursor Mode" target="cursor"/>
+	<tocitem text="What's new" target="new" expand="true">
+      <tocitem text="Release History" target="release"/>
+	  <tocitem text="PDB Viewing with Jmol" target="pdbjmol"/>
+	  <tocitem text="Mapping between Sequences" target="seqmappings"/>
+    </tocitem>
+    <tocitem text="Editing Alignments" target ="edit"/>	
+    <tocitem text="Cursor Mode" target="cursor"/>
 	<tocitem text="Key Strokes" target="keys"/>
 	<tocitem text="Input / Output" target="io"/>
   	<tocitem text="Making figures" target="export"/>
 	<tocitem text="Hidden Regions" target="hiddenRegions"/>
-	<tocitem text="Viewing PDB Files" target="viewingpdbs"/>
 	<tocitem text="Multiple Views" target="multipleviews"/>
 	<tocitem text="Sequence Features" target="seqfeatures" expand="false">
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
@@ -61,6 +63,10 @@
           <tocitem text="Consensus" target="calcs.consensus"/>
           <tocitem text="Annotations File Format" target="annotations.fileformat"/>
         </tocitem>
+	<tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
+	  <tocitem text="Jmol Viewer" target="pdbjmol"/>
+	  <tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
+	</tocitem>
 	<tocitem text="Window Menus" target="menus" expand="false">
 		<tocitem text="Desktop Window" target="desktopMenu"/>
 		<tocitem text="Alignment Window" target="alMenu">
@@ -76,11 +82,15 @@
 		<tocitem text="Popup Menu" target="popMenu"/>
                 </tocitem>
 	</tocitem>
+        <tocitem text="Preferences" target="preferences"/>
 	<tocitem text="Memory Settings" target="memory" expand="false">
           <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
           </tocitem>
+        <tocitem text="Command Line" target="commandline" expand="false">
+          <tocitem text="Command Line Arguments" target="clarguments"/>
+        </tocitem>
 </tocitem>
-<tocitem text="Useful information" expand="true">
+<tocitem text="Useful information" expa nd="true">
 	<tocitem text="Amino Acid Table" target="aminoAcids"/>
 	<tocitem text="Amino Acid Properties" target="aaProperties"/>
 	<tocitem text="The Genetic Code" target="geneticCode"/>