X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpreferences.html;h=acd7ba698dac33958efe7f0a1296b9bb76786271;hb=a15893b027f58f6b616448be6328b904d6cc56d9;hp=fb2183641dc866450d6945ee5349b577db00f18c;hpb=3c2ee3e1b9c507c7dfa550bc8546a43ff305f85a;p=jalview.git

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index fb21836..acd7ba6 100755
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -89,10 +89,11 @@
   <p>
     <em>Show Annotations</em> - If this is selected the new window will
     display an annotation panel below the sequences. This annotation
-    panel may have several rows describing the whole alignment. The 3
-    standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em>
-    for the alignment may be shown or hidden by default using the
-    checkboxes below.
+    panel may have several rows describing the whole alignment. The 4
+    standard annotations <em>Conservation</em>, <em>Quality</em>, 
+    <em>Occupancy</em> and <em>Consensus</em> for the alignment may 
+    be shown or hidden by default using the checkboxes adjacent and
+    below.
   </p>
   <p>
     <em>Show group: Conservation and Consensus</em> controls the display
@@ -260,7 +261,11 @@
     The <em>Custom only</em> button limits the entries in the table to
     just those you have configured yourself <em>via</em> the <em>Edit
       Links</em> buttons. Press <em>Show all</em> to clear any filters.
-  <p>
+  </p>
+  <p>The links table is prepoulated with persistent URLs for many common
+    bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from
+    the <em>identifiers.org</em> website, and the names and URLs are not
+    user editable.
     <a href="../webServices/urllinks.html#urllinks">Read more about configuring
       URL links.</a>
   </p>
@@ -332,7 +337,7 @@
     and PDB file association (if available). The Jalview id/start-end
     option is ignored if Modeller output is selected.
   <p>
-    <a name="editing"><strong>Editing Preferences tab</strong></a>
+    <a name="editing"><strong>e&quot;Editinge&quot; Preferences tab</strong></a>
   </p>
   <p>There are currently three options available which can be
     selected / deselected.</p>