Merge branch 'develop' into feature/r2_11_2/JAL-3808_gff2_exonerate

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

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index a0c7fe6..9f1942c 100755 (executable)
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -27,7 +27,7 @@
         <tocitem text="Virtual Features in CDS/Protein Views" target="splitframe.virtualfeats"/>
                                <tocitem text="VCF Variant Attributes" target="importvcf.attribs"/>
                                <tocitem text="Feature Filters and Attribute Colourschemes" target="features.featureschemes" />
-                               
+        <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
                </tocitem>
                
                <tocitem text="Editing Alignments" target="edit" />
@@ -131,9 +131,10 @@
                </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 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">
@@ -156,6 +157,7 @@
                        </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>