X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2FhelpTOC.xml;h=59d30e4db4122dd5b287e490eec361c0737eadee;hb=649c3dff0ddf4047b11e83950642501897c60d5c;hp=5252a302d01ae0c96e0581482a5c464547011403;hpb=96b6991703b70a1bbb0491f9946d397c9fcf5a38;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 5252a30..59d30e4 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -3,25 +3,21 @@
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
 	<tocitem text="What's new" target="new" expand="true">
-	  <tocitem text="Multiple Views" target="multipleviews"/>
-	  <tocitem text="New keystrokes and Menus" target="newkeys"/>
-	  <tocitem text="Reload and Save" target="reloadsave"/>
-	  <tocitem text="Creating Sequence Features" target="seqfeatcreat"/>
-	  <tocitem text="Amending or Deleting Sequence Features" target="seqfeatedit"/>
-      <tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
-          </tocitem>
-        <tocitem text="Release History" target="release"/>
-        <tocitem text="Editing Alignments" target ="edit"/>	
-        <tocitem text="Cursor Mode" target="cursor"/>
+      <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"/>
           <tocitem text="Sequence Features File" target="features.fileformat"/>
-          <tocitem text="User Defined Sequence Features" target="search"/>
+          <tocitem text="User Defined Sequence Features" target="seqfeatcreat"/>
 		  <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
           <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
 	  <tocitem text="DAS Feature Settings" target="das.settings"/>
@@ -36,6 +32,7 @@
           <tocitem text="Secondary Structure Prediction" target="jnet"/>
 	</tocitem>
 	<tocitem text="Colour Schemes" target="colours" expand="false">
+		<tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
 		<tocitem text="ClustalX" target="colours.clustal"/>
 		<tocitem text="Zappo" target="colours.zappo"/>
 		<tocitem text="Taylor" target="colours.taylor"/>
@@ -66,6 +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">
@@ -81,11 +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"/>