2.2 documentation

diff --git a/help/html/features/hiddenRegions.html b/help/html/features/hiddenRegions.html
index 66413d9..3f7b599 100644 (file)
--- a/help/html/features/hiddenRegions.html
+++ b/help/html/features/hiddenRegions.html
@@ -24,9 +24,13 @@ the sequences in that group. <br>
 The hidden representative sequences will not be used in any calculations
 or web service alignments (<em>nb. this may change in the future</em>).
 <br>
-<strong>Warning:</strong>The representative sequence groups feature is
-not fully implemented in the jalview 2.2 release, following the
-introduction of Multiple views.</p>
+<blockquote><em><strong>Warning:</strong>hidden
+representative sequence groups are only partly implemented in the
+jalview 2.2 release. When a hidden representative group is created in
+one alignment view, it will be propagated to all other views. Similarly,
+revealing the represented sequences in one view will reveal them in all
+other views. This will be resolved in a future Jalview release. </em></blockquote>
+</p>
 <p><strong><em>Hiding Columns</em></strong><br>
 To hide selected columns in an alignment, use the <strong>&quot;View
 -&gt; Hide -&gt; Selected Columns&quot;</strong> menu item, or right click within

diff --git a/help/html/features/multipleViews.html b/help/html/features/multipleViews.html
index 36bda32..7b17d06 100644 (file)
--- a/help/html/features/multipleViews.html
+++ b/help/html/features/multipleViews.html
@@ -40,11 +40,13 @@ to any or all other views.</p>
 calculation</a> on a particular view may also be associated with other
 views, using the PCA Viewer's <strong>&quot;View&#8594;Associate
 Nodes&quot;</strong> submenu.</p>
-<p>A <a href="pdbviewer.html">PDB Structure Viewer</a> opened on a
-structure associated with a sequence in a particular view will also, by
-default, only be associated with the sequence as it is displayed in that
-view. The &quot;View&#8594;Associate View&quot; submenu allows the
-association of alternative views.</p>
+<p>Currently, a <a href="pdbviewer.html">PDB Structure Viewer</a>
+opened on a structure associated with a sequence in a particular view
+will only be associated with the seuqence as displayed in that view. <br><em>This
+will be resolved in a future release</em><!-- also, by default, only be associated
+with the sequence as it is displayed in that view. The
+&quot;View&#8594;Associate View&quot; submenu allows the association of
+alternative views.</p> -->
 <p><em>Multiple Views were introduced in Jalview 2.2</em></p>
 </body>
 </html>

diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html
index 97471a2..9e1e6e5 100755 (executable)
--- a/help/html/features/pdbviewer.html
+++ b/help/html/features/pdbviewer.html
@@ -8,7 +8,8 @@
 the <strong>&quot;Sequence&#8594;View PDB entry:&quot;</strong> entry in
 the <a href="../menus/popupMenu.html">sequence id pop-up menu</a>. This
 can only be done for sequences which have an <a href="viewingpdbs.html">associated
-PDB structure</a>.</p>
+PDB structure</a>, and the PDB Viewer will only be associated with the
+particular alignment view from which it was opened.</p>
 <p><strong>Controls</strong></p>
 <p>The structure is rendered as an alpha-carbon trace. Moving the
 mouse over the structure brings up tooltips with a residue name and PDB
@@ -121,9 +122,9 @@ and alpha carbon location.</p>
                <li><strong>Show All Chains<br>
                </strong><em> When turned on, shows all chains in the PDB file, not just
                the one associated with a sequence in the alignment window.</em></li>
-               <li><strong>Associate View</strong><br>
+               <!--  NOT YET IMPLEMENTED <li><strong>Associate View</strong><br>
                Change which view on the associated sequence's alignment is to be
-               associated with the PDB viewer.
+               associated with the PDB viewer.-->
        </ul>
        </li>
 </ul>

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index ef222b1..4b4920d 100755 (executable)
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -1,32 +1,32 @@
-<html>\r
-<head><title>PDB Viewing</title></head>\r
-<body>\r
-<p><strong>Viewing PDB Structures</strong></p>\r
-<p>Jalview has a simple <a href="pdbviewer.html">3D structure viewer</a> which can visualize polypeptide backbone\r
-  structures associated with a sequence in an alignment. It is\r
-  accessed via the <strong>&quot;Sequence&#8594;View PDB\r
-  entry:&quot;</strong> entry from the sequence's <a\r
-  href="../menus/popupMenu.html">pop-up menu</a>.</p>\r
-<p>To associate PDB files with a sequence, right click on a sequence ID and select \r
-  &quot;Associate Structure with Sequence&quot;, and one of the submenus:</p>\r
-<ul>\r
-  <li>From File - You can load a PDB file from the local machine or network and \r
-    associate it with the selected sequence. PDB files associated in this way \r
-    can be saved in the Jalview Archive file. <br>\r
-  </li>\r
-  <li>Enter PDB Id - Jalview will use WSDBFetch, provided by the EBI, to fetch \r
-    the PDB file with the entered Id.<br>\r
-  </li>\r
-  <li>Discover PDB Ids - Jalview uses WSDBFetch, provided by the EBI, to discover \r
-    PDB ids for all the sequences in the alignment which have valid Uniprot names \r
-    / accession ids. </li>\r
-</ul>\r
-<p><strong>Note:</strong> You can retrieve sequences from the PDB using the <a\r
-  href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with this \r
-  service are automatically associated with their source database entry. For PDB \r
-  sequences, simply select PDB as the database and enter your known PDB id (appended \r
-  with ':' and a chain code, if desired).</p>\r
-<p>For help on viewing and colouring structures see the <a\r
-href="pdbviewer.html">PDB Viewer</a> help page. </p> </p>\r
-</body>\r
-</html>\r
+<html>
+<head><title>PDB Viewing</title></head>
+<body>
+<p><strong>Viewing PDB Structures</strong></p>
+<p>Jalview has a simple <a href="pdbviewer.html">3D structure viewer</a> which can visualize polypeptide backbone
+  structures associated with a sequence in a particular alignment view. It is
+  accessed via the <strong>&quot;Sequence&#8594;View PDB
+  entry:&quot;</strong> entry from the sequence's <a
+  href="../menus/popupMenu.html">pop-up menu</a>.</p>
+<p>To associate PDB files with a sequence, right click on a sequence ID and select 
+  &quot;Associate Structure with Sequence&quot;, and one of the submenus:</p>
+<ul>
+  <li>From File - You can load a PDB file from the local machine or network and 
+    associate it with the selected sequence. PDB files associated in this way 
+    can be saved in the Jalview Archive file. <br>
+  </li>
+  <li>Enter PDB Id - Jalview will use WSDBFetch, provided by the EBI, to fetch 
+    the PDB file with the entered Id.<br>
+  </li>
+  <li>Discover PDB Ids - Jalview uses WSDBFetch, provided by the EBI, to discover 
+    PDB ids for all the sequences in the alignment which have valid Uniprot names 
+    / accession ids. </li>
+</ul>
+<p><strong>Note:</strong> You can retrieve sequences from the PDB using the <a
+  href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with this 
+  service are automatically associated with their source database entry. For PDB 
+  sequences, simply select PDB as the database and enter your known PDB id (appended 
+  with ':' and a chain code, if desired).</p>
+<p>See the <a
+href="pdbviewer.html">PDB Viewer</a> help page for more information. </p> </p>
+</body>
+</html>