X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=679f35303af73c34f709b32761589352d37c64b0;hb=96433cd123131e1a572be3bce03be00d61367876;hp=71c201154d44a1905fa88068e0089e22de2dc991;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index 71c2011..679f353 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -44,8 +44,17 @@ structure is selected, one of the following will happen:</p>
 	PDB viewer</a> help page for more information about the display.</li>
 </ul>
 
+	<p>
+		Additionally, if several of the sequences in the currently selected
+		region of the alignment have associated structures, then Jalview will
+		provide a 'View <em>X</em> structures' entry in the submenu. This
+		option will open a new Jmol view containing all the structures
+		available for all selected sequences, superimposed using the currently
+		selected region of the alignment. (<em>This capability was added
+			in Jalview 2.7</em>)
+	</p>
 
-<p>To associate PDB files with a sequence, right click on a sequence
+	<p>To associate PDB files with a sequence, right click on a sequence
 ID and select "Structure<strong>&rarr;</strong> Associate Structure with
 Sequence", and one of the submenus:</p>
 
@@ -75,6 +84,18 @@ Jalview will also read PDB files directly. Simply load in the file as
 you would an alignment file. The sequences of any peptide chains will be
 extracted from the file and viewed in the alignment window.</p>
 
+<p>
+<strong>Associating a large number of PDB files to sequences
+in an alignment</strong><br /> It is often the case when working with
+structure alignments that you will have a directory of PDB files, and
+an alignment involving one or more of the structures. If you drag a
+number of PDB files onto an alignment in the Jalview desktop, Jalview
+will give you the option of associating PDB files with sequences that
+have the same filename. This means, for example, you can automatically
+associate PDB files with names like '1gaq.pdb' with sequences that
+have an ID like '1gaq'.
+<br/><em>Note: This feature was added in Jalview 2.7</em>
+</p>
 <p><em>Note for jalview applet users:<br>
 Due to the applet security constraints, PDB Files can currently only be
 imported by cut and paste of the PDB file text into the text box opened
@@ -90,11 +111,11 @@ Features"</strong> menu item and the <a href="featuresettings.html">Feature
 Settings dialog box</a>.</p>
 
 <p><em><strong>Outstanding problem with cut'n'pasted
-files in Jalview 2.6</strong><br>
+files in Jalview 2.6 and Jalview 2.7</strong><br>
 Structures imported via the cut'n'paste dialog box will not be correctly
 highlighted or coloured when they are displayed in structure views,
 especially if they contain more than one PDB structure. See the bug
-report at http://issues.jalview.org/JAL-623 for news on this problem.</em></p>
+report at http://issues.jalview.org/browse/JAL-623 for news on this problem.</em></p>
 </body>
 </html>
 
