X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=736e786392803ba2652d9dd8f443a0b37793bda4;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=d124cc8d5de3e7904164dc87fd7fd9e7f48271db;hpb=9a881df532ecf49063d4f032144533b9a1a89319;p=jalview.git

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index d124cc8..736e786 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -30,13 +30,12 @@
     Jalview 2.9 has been in development since December 2014. In addition
     to a multitude of bug fixes and minor improvements (both small, and
     rather big!), it also brings major new capabilities for codon-level
-    analysis of protein alignments and the manipulation of structural
-    data.<br />For the full list of changes, see the <a
-      href="releases.html#Jalview.2.9">Jalview 2.9 Release Notes</a>.
+    analysis of protein alignments and the retrieval and manipulation of
+    structural data.</p><p>For the full list of changes, see the
+    <a href="releases.html#Jalview.2.9">Jalview 2.9 Release Notes</a>.
   </p>
   <p>
     <strong>Highlights in Jalview 2.9</strong>
-  
   <ul>
     <li><strong>Visualisation, editing and analysis of
         cDNA and Protein alignments</strong><br />A new <a
@@ -46,8 +45,8 @@
       reconstructed from protein alignments calculated by Jalview's web
       services, and update in response to edits in the amino acid view.<br />To
       start experimenting with cDNA/Protein analysis, jut drop a file
-      containing cDNA sequences which code for, and have IDs matching
-      proteins in an existing alignment, and Jalview will do the rest.</li>
+      containing cDNA sequences which code for proteins in an existing
+      alignment, and Jalview will do the rest.</li>
     <li><strong>Enhanced Integration of UCSF Chimera</strong> <br>Jalview
       2.9 provides full support for the use of Chimera to view 3D
       structures linked to alignment views in the Jalview Desktop. We've
@@ -59,7 +58,7 @@
       much more responsive, and selected regions in Chimera are now
       shown as highlighted regions in the Jalview desktop.</li>
     <li><strong>Interactive querying of the PDBe</strong><br />Jalview
-      users can now browse and retrieve 3D structure data from the PDB
+      users can now <a href="features/pdbsequencefetcher.html">browse</a> and <a href="features/viewingpdbs.html">retrieve 3D structure</a> data from the PDB
       via the <a href="http://www.ebi.ac.uk/pdbe/api/doc/search.html">PDBe
         Search API</a> (<a href="http://dx.doi.org/10.1093%2Fnar%2Fgkt1180">Gutmanas
         et al 2014</a>). Developed in collaboration with the PDBe group at
@@ -69,18 +68,19 @@
       criteria.</li>
     <li><strong>Improved support for RNA visualisation</strong><br />Jalview
       2.9 integrates the latest version of the <a
-      href="http://varna.lri.fr">VARNA RNA Viewer</a>, and VARNA views
+      href="features/varna.html">VARNA RNA Viewer</a>, and VARNA views
       can also now be stored in Jalview projects. We've also dealt with
       a number of lingering bugs in the VARNA/Jalview interface,
       including the loss of pseudoknots when RNA secondary structure is
       shown VARNA.</li>
     <li><strong>Protein Secondary Structure predictions
-        with JPred4</strong>Jalview includes a number of new features for working
-      with secondary structure predictions from the JPred4 server. These
-      include the ability to automatically hide insertions and highlight
-      mutations in an alignment with respect to a reference sequence.
-      Jalview 2.9's new scrollable SVG HTML export mode was also
-      developed specifically for the JPred4 server.</li>
+        with JPred4</strong><br />Jalview includes a number of new features for
+      working with secondary structure predictions from the JPred4
+      server. These include new <a href="menus/popupMenu.html#hideinserts">popup menu actions</a> to automatically hide insertions and highlight
+      mutations in an alignment with respect to a <a href="calculations/referenceseq.html">Reference
+        Sequence</a>. Jalview 2.9's new <a href="io/export.html#htmlexport">scrollable
+        SVG HTML export</a> was also developed specifically for the JPred4
+      server.</li>
   </ul>
 
 </body>
