JAL-3608 JAL-3830 tweaked the what’s new text and updated helpTOC

[jalview.git] / help / help / helpTOC.xml

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 5374e1a..a9b9788 100755 (executable)
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -24,9 +24,12 @@
        <tocitem text="Jalview Documentation" target="home" expand="true">
                        <tocitem text="What's new" target="new" expand="true">
                                <tocitem text="Latest Release Notes" target="release"/>
-                               <tocitem text="VCF Variant Attributes" target="importvcf.attribs"/>
-                               <tocitem text="Feature Filters and Attribute Colourschemes" target="features.featureschemes" />
-                               
+                       <tocitem text="Support for ChimeraX" target="chimera"/>
+                               <tocitem text="Support for Pymol" target="pymol"/>
+                               <tocitem text="Structures via 3D Beacons" target="structuresvia3dbeacons" />
+                               <tocitem text="Startup Memory Settings" target="startupprefs" />
+                       <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
+                       <tocitem text="Command line launch scripts" target="jalviewcltool"/>
                </tocitem>
                
                <tocitem text="Editing Alignments" target="edit" />
@@ -62,6 +65,7 @@
                        <tocitem text="Feature Colourschemes" target="features.featureschemes" />
                        <tocitem text="User Defined Sequence Features" target="seqfeatcreat" />
                        <tocitem text="Editing Sequence Features" target="seqfeatedit" />
+                       <tocitem text="HTML Feature Attributes report" target="seqfeatures.report" />
                        <tocitem text="HTML annotation report" target="io.seqreport" />
                </tocitem>
                
@@ -129,9 +133,10 @@
                </tocitem>
                <tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
                        <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
-                       <tocitem text="PDB Structure Chooser" target="pdbchooser" />
+                       <tocitem text="PDB &amp; 3D-Beacons Structure Chooser" target="pdbchooser" />
                        <tocitem text="Jmol Viewer" target="pdbjmol" />
-                       <tocitem text="Chimera Viewer" target="chimera" />                      
+                       <tocitem text="Chimera/X Viewer" target="chimera" />
+                       <tocitem text="Pymol Viewer" target="pymol" />                  
                </tocitem>
                <tocitem text="Viewing RNA structures" target="varna" expand="false"/>
                <tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
@@ -154,6 +159,7 @@
                        </tocitem>
                </tocitem>
                <tocitem text="Preferences" target="preferences" />
+    <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
                <tocitem text="Scripting with Groovy" target="groovy">
                        <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
                </tocitem>