X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=d9d25f4735f565a28dd0a1821cb306a505e1c483;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=4ca6e935759401997d83f81d473a307640cceb5a;hpb=1a703959b2bfba03cf8117466f8f98f9aba1e77c;p=jalview.git

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 4ca6e93..d9d25f4 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -31,10 +31,78 @@
 		development team.<br /> It incorporates many minor improvements and
 		bug-fixes, and new features for working with 3D structure data,
 		shading alignments by secondary structure and generation of alignment
-		figures as Scalable Vector Graphics.
-		<br />As ever, the highlights are detailed below, and the full list is
-		given in the
-		<a href="releases.html#Jalview2.8.2">Jalview 2.8.2 Release Notes</a>.
+		figures as Scalable Vector Graphics. <br />The majority of
+		improvements in this version of Jalview concern the desktop
+		application. As ever, the highlights are detailed below,
+		and the full list is given in the <a
+			href="releases.html#Jalview.2.8.2">Jalview 2.8.2 Release Notes</a>.
 	</p>
+	<p>
+		<strong>Annotation visualisation</strong> <br /> The alignment window
+		includes a new <em>Annotations</em> menu which provides controls for
+		the layout and display of sequence, group and alignment associated
+		annotation rows. It also now includes the <em>Autocalculated
+			Annotation</em> submenu (formerly located in the View menu), which
+		includes settings for the calculation and display of sequence
+		consensus, logos, and amino acid conservation for the alignment and
+		subgroups.
+	</p>
+	<p>
+		<strong>Sequence associated annotation</strong><br /> New controls
+		have also been added to the Sequence ID popup menu for the propagation
+		and display of sequence associated annotation such as secondary
+		structure assignments and disorder predictions. Annotation associated
+		with one or a group of sequence already shown on the alignment may be
+		shown or hidden, and any available annotation from 3D structure or
+		calculations performed in other Jalview windows can be copied to the
+		alignment
+		<em>via</em> the <strong>Add Reference Annotation</strong> option.<br />
+		The <strong>Colour by annotation</strong> function has also been
+		improved, allowing secondary structure annotation to be used to shade
+		sequences and alignment columns. Protein sequences can be coloured
+		according to the presence of a helix or sheet at each position, and
+		RNA sequences can be shaded according to each structure's stem/helix
+		pattern - which enables different RNA folding topologies to be quickly
+		identified.
+	</p>
+	<p>
+		<strong>3D Structural data analysis and display</strong><br />
+		Jalview now employs Jmol's PDB data API to retrieve secondary
+		structure assignments made by the DSSP algorithm. It can also employ
+		web services to obtain secondary structure assignments from RNA
+		structures. These assignments are shown as sequence associated
+		annotation for sequences which have cross-references to the PDB, or
+		have had PDB files associated with them via the <em>Structures</em>
+		submenu of the sequence ID popup menu. The extraction and display of
+		secondary structure and B-factor column annotation is controlled <em>via</em>
+		a new <strong>Structure</strong> tab in the Jalview Desktop's
+		Preferences dialog box.
+	</p>
+	<p>
+		<Strong>Interoperation with UCSF Chimera</Strong><br /> The desktop
+		application can now be configured to employ UCSF Chimera for the
+		display of 3D structure data. UCSF Chimera is a python-based
+		high-performance molecular graphics and animation system developed by
+		the Resource for Biocomputing, Visualisation, and Informatics at the
+		University of California.<br />Jalview employs the 'StructureViz'
+		communication mechanism developed for Cytoscape by Morris et al.
+		(http://www.ncbi.nlm.nih.gov/pubmed/17623706) in 2007. This mechanism
+		allows Jalview to send commands to Chimera, enabling structures to be
+		superimposed and shaded according to associated multiple aligmment
+		views. <br />Support for Chimera in Jalview 2.8.2 is experimental, and we
+		would appreciate feedback ! Please send your comments to
+		jalview-discuss@jalview.org, and keep up to date with this feature's
+		development via http://issues.jalview.org/browse/JAL-1333.
+	</p>
+	<p>
+		<strong>Export of alignment figures as Scalable Vector
+			Graphics</strong> <br />Scalable Vector Graphics (SVG) files are now widely
+		supported by web browsers and graphics design programs, and allow
+		high-quality graphics for interactive exploration and publication.
+		Jalview now supports the generation of SVGs interactively (via the
+		Export) menu, and from the command line for server-side figure
+		generation.
+	</p>
+
 </body>
 </html>
