Merge branch 'features/JAL-1667_1668-documentation' into Release_2_8_3_Branch

diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index 31ca419..11b43c8 100644 (file)
--- a/help/html/features/chimera.html
+++ b/help/html/features/chimera.html
@@ -32,7 +32,7 @@ id pop-up menu</a> (if you can't see this, then you need to <a
 sequence). Chimera is available from the Jalview desktop, provided Chimera has been separately installed.</p>
 <p>You can set a default choice of Jmol or Chimera structure viewer in <a href="preferences.html#structure"> Preferences</a>. 
 You can also optionally specify the path to the Chimera program here (if it differs from the standard paths searched by Jalview).
-<p>The following menu entries are provided for viewing structure data<br>
+<!-- <p>The following menu entries are provided for viewing structure data<br>
   <ul>
     <li>The <strong>&quot;Structure&#8594;View
         Structure&#8594;</strong> submenu allows a single PDB structure to be chosen
@@ -49,10 +49,10 @@ You can also optionally specify the path to the Chimera program here (if it diff
       currently selected sequence.<br /></li>
   </ul>
   <br> 
-</p>
+</p> -->
 <p><a name="align"><strong>Superposing structures based
 on their aligned sequences</strong></a><br>
-<p>If several structures are available on the alignment, you may add
+If several structures are available on the alignment, you may add
 additional structures to an existing Chimera view by selecting their entry
 in the appropriate pop-up menu. Jalview will ask you if you wish to add
 the structure to the existing alignment, and if you do, it will import
@@ -63,12 +63,12 @@ menu bar of the structure view window to superpose the structures using
 the updated alignment.<br>
 </p>
 <p><strong>Chimera Controls</strong><br>
-<p>The structure is by default rendered as a ribbon diagram. Moving the
+The structure is by default rendered as a ribbon diagram. Moving the
 mouse over the structure brings up tooltips giving the residue name, PDB
 residue number and chain code
 ([RES]Num:Chain). Moving the mouse over an
 associated residue in an alignment window highlights the associated
-atoms in the displayed structures. For comprehensive details of Chimera's commands, refer to the tool's Help menu.</p>
+atoms in the displayed structures. For comprehensive details of Chimera's commands, refer to the tool's Help menu.
 <p>Basic screen operations (see <a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html">Chimera help</a> 
 (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html) for full details).
 <table border="1">

diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html
index ce1b834..c81fcc3 100644 (file)
--- a/help/html/features/jmol.html
+++ b/help/html/features/jmol.html
@@ -33,7 +33,7 @@ sequence). Jmol is available from the Jalview desktop and should also
 run in the JalviewLite applet, providing the browser supports Java 1.5.
 If Jmol is not available, then the original <a href="pdbviewer.html">internal
 pdb viewer</a> will be used as a fallback.</p>
-<p>The following menu entries are provided for viewing structure data<br>
+<!-- <p>The following menu entries are provided for viewing structure data<br>
   <ul>
     <li>The <strong>&quot;Structure&#8594;View
         Structure&#8594;</strong> submenu allows a single PDB structure to be chosen
@@ -52,7 +52,7 @@ pdb viewer</a> will be used as a fallback.</p>
         Jalview 2.8.1</em></li>
   </ul>
   <br> 
-</p>
+</p> -->
 <p><a name="align"><strong>Superposing structures based
 on their aligned sequences</strong></a><br>
 If several structures are available on the alignment, you may add

diff --git a/help/html/features/pdbseqfetcher.png b/help/html/features/pdbseqfetcher.png
new file mode 100644 (file)
index 0000000..b243168
Binary files /dev/null and b/help/html/features/pdbseqfetcher.png differ

diff --git a/help/html/features/pdbsequencefetcher.html b/help/html/features/pdbsequencefetcher.html
new file mode 100644 (file)
index 0000000..0412a5f
--- /dev/null
+++ b/help/html/features/pdbsequencefetcher.html
@@ -0,0 +1,83 @@
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>PDB Sequence Fetcher</title>
+</head>
+<body>
+
+       <strong>PDB Sequence Fetcher</strong>
+       <p>From Jalview 2.x.x a speciliased interface was introduced for
+               fast and efficient discovery/retrieval of sequence data from the PDB
+               database. The introduced interface enables live querying of PDB data
+               on-the-fly thereby eliminating the need to memorise database accession
+               or to cross-reference other bioinformatics websites before retrieving
+               a sequence data in jalview. The underlying technology is provided by
+               EBI and is based on Apache Solr which is a text based search engine.</p>
+
+       <p>
+               The PDB Sequence Fetcher interface can be opened by selecting <strong>PDB</strong>
+               as the choice database from the <strong>'Select Database
+                       Retrieval Source'</strong> interface of <a href="seqfetch.html">Sequence
+                       Fetcher</a>.
+       </p>
+
+       <img src="pdbseqfetcher.png" align="left"
+               alt="PDB sequence fetcher (introduced in Jalview 2.x.x)">
+
+
+       <p>
+               <strong>Searching the PDB Database</strong><br> Once the
+               interface is opened, typing in the search text box will execute a live
+               query to the PDB database and display the results on-the-fly as seen
+               in the screen-shot above. Use the drop-down menu to select a specific
+               field to search by in the PDB database, the default option is <strong>'ALL'</strong>.
+       <br>
+       
+       <br>Wild card searching: The PDB sequence fetcher also provides support for wild card querying of the PDB database.
+       <br>Single character (matches a single character) - ?
+ The search string te?t would match both test and text.
+
+<br>Multiple characters (matches zero or more sequential characters) - *
+
+The wildcard search:
+tes*  - would match test, testing, and tester.
+
+
+You can also use wildcard characters in the middle of a term. For
+example:
+te*t - would match test and text.
+*est  - would match pest and test.
+ </p>
+ 
+       <p>
+               <strong>Customising displayed meta-data</strong> <br>To change the
+               displayed meta-data in the search result, click the <strong>'Configure
+                       Displayed Columns'</strong> tab, then tick off the options wanted. 
+       </p>
+       <p><strong>Importing Sequence</strong><br>
+       After querying the PDB database, to import the found data into Jalview, select the entries you wish to import then click the ok button at the bottom of the interface.</p>
+       <p>
+               <em>The PDB Sequence Fetcher interface was introduced in Jalview
+                       2.x.x.</em>
+       </p>
+</body>
+</html>
\ No newline at end of file

diff --git a/help/html/features/schooser_enter-id.png b/help/html/features/schooser_enter-id.png
new file mode 100644 (file)
index 0000000..dc5aa93
Binary files /dev/null and b/help/html/features/schooser_enter-id.png differ

diff --git a/help/html/features/schooser_main.png b/help/html/features/schooser_main.png
new file mode 100644 (file)
index 0000000..fe9e5dc
Binary files /dev/null and b/help/html/features/schooser_main.png differ

diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html
index fa61e1a..68c5520 100755 (executable)
--- a/help/html/features/seqfetch.html
+++ b/help/html/features/seqfetch.html
@@ -49,6 +49,7 @@ WSDBFetch service provided by the European Bioinformatics Institute, or, since J
   one or more accession ids (as a semi-colon separated list), or press the 
   "Example" button to paste the example accession for the currently selected database into the retrieval box.
    Finally, press &quot;OK&quot; to initiate the retrieval.</p>
+   <p>Since Jalview 2.x.x if  PDB is selected as the sequence database, a specialised interface - <a href="pdbsequencefetcher.html">PDB Sequence Fetcher</a>  is used for discovering and retrieving the sequenec data. </p>
        <p><strong>Specifying chains for PDB IDs</strong>
   If you are retrieving sequences from the PDB, you can retrieve
   specific chains by appending a colon and the chain id to the PDB

diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html
new file mode 100644 (file)
index 0000000..7dd69c1
--- /dev/null
+++ b/help/html/features/structurechooser.html
@@ -0,0 +1,109 @@
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Structure Chooser</title>
+</head>
+
+<body>
+       <p>
+               <strong>Structure Chooser</strong>
+       </p>
+
+       The Structure Chooser interface provides a smart technique for
+       selecting PDB structures to view in Jalview by querying readily
+       available meta-data of structures. The Interface  can be invoked by selecting
+       the
+       <strong>"View Structure"</strong> option from a sequence's
+       <a href="../menus/popupMenu.html">pop-up menu</a>. Some of the main
+       features it provides are listed below:
+       <ul>
+               <li>Automatic discovery, retrieval and association of PDB entries
+                       for an alignment's sequences</li>
+               <li>Visualisation of discovered structures' meta-data</li>
+               <li>Ability to configure the meta-data entries to visualise</li>
+               <li>Auto-selection of the best structure via filtering by the
+                       available metric parameters in the meta-data (i.e. resolution,
+                       quality etc).</li>
+               <li>Selection of multiple structures in a single operation</li>
+       </ul>
+       Additionally, the Structure Chooser retains the following contemporary
+       features of Jalview:
+       <ul>
+               <li>Manual association of PDB entries via entering the PDB Id or
+                       From File</li>
+               <li>Ability to view cached PDB entries</li>
+       </ul>
+
+
+       <strong>Associating PDB files with Sequences</strong><br>
+       Discovery/Association of PDB entries to a sequence happens
+       automatically during the initialisation of the Structure Chooser
+       Interface. Jalview uses the sequence's ID to query the PDB Rest API,
+       provided by the EBI to discover PDB Ids associated with the sequence.
+
+<br><br>
+       <strong>Configuring displayed  meta-data for  Structures</strong><br>
+       To configure the visible meta-data displayed for the discovered structures, click the <strong>'Configure Displayed Columns'</strong> tab, then tick the options which you intend to make visible.
+
+<br><br>
+       <strong>Auto-selection of best Structures</strong>
+       <br> Jalview can automatically filter and select the best structures using various metric categories avaialble from the meta-data
+       of the structures. To perform this simply select any of the following options from the drop-down menu in the Structure
+       Chooser interface: Best Uniprot coverage, Higest Resolution, 
+
+       Best Quality, Highest Protein Chain etc. When the <strong>'Invert'</strong> option is selected, Jalview returns an inverse result for the current selected option in the drop-down menu.<p>
+               <img src="schooser_main.png" style="width: 464px; height: 369px;">
+               <!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
+       <p><img src="schooser_drop-down.png" style="width: 464px; height: 368px; ">
+       <p><img src="schooser_enter-id.png" style="width: 467px; height: 373px; ">
+       <p><img src="schooser_from-file.png" style="width: 468px; height: 370px; ">
+       <p><img src="schooser_cached.png"> -->
+               <br>The screenshot above shows the Structure Chooser interface
+               along with the meta-data of auto-discovered structures for the sample
+               alignment. Note however that if no structures were auto-discovered, a
+               different interface for manual association will be invoked as seen in
+               the screenshot below.
+       <p>
+               <img src="schooser_enter-id.png" style="width: 464px; height: 369px;">
+       <p>
+               <strong>Manual selection/association of PDB files with Sequences</strong>
+       </p>
+       <p>To manually associate PDB files with a sequence, select any of
+               the follwing options listed below from the drop-down menu in the
+               interface:
+       <ul>
+               <li><strong>From File</strong> - 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 will also be saved in the <a
+                       href="jalarchive.html">Jalview Archive file</a>.<br></li>
+               <li><strong>Enter PDB Id</strong> - Jalview will use the PDB Rest
+                       API, provided by the EBI, to fetch the PDB file with the entered Id.<br>
+               </li>
+               <li><strong>Cached PDB Entries</strong> - You can view PDB structures which have previously been downloaded/viewed using this option. Jalview caches  previously downloaded PDB entries in the computer memory. However, if the project is saved before exiting Jalview, Jalview will serialize the cached entries to the file system. </li>
+       </ul>
+
+       <p>
+               <em>The Structure Chooser interface was introduced in Jalview 2.x.x.
+               </em>
+       </p>
+</body>
+</html>
\ No newline at end of file

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index c342bc9..506beef 100755 (executable)
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -23,12 +23,29 @@
 <title>PDB Viewing</title>
 </head>
 <body>
-<p><strong>Viewing PDB Structures</strong></p>
        <p>
-               Jalview can view protein structures associated with a sequence via the
-               <strong>"Structure&rarr;"</strong> submenu from a sequence's <a
-                       href="../menus/popupMenu.html">pop-up menu</a>.
+               <strong>Viewing PDB Structures</strong>
        </p>
+       Jalview can be used to view protein structures by following the steps below:
+       <ol>
+               <li>Select the <strong>"View Structure"</strong> option from a
+                       sequence's <a href="../menus/popupMenu.html">pop-up menu</a> to invoke the <a href="structurechooser.html">Structure Chooser</a> interface.
+                       <ul>
+                               <li>If one or more structures exists for the given sequence, the <a href="structurechooser.html">Structure Chooser</a>
+                                       dialogue is opened with a list of the found structures meta-data.</li>
+                               <li>However, if no structure was found, the <a href="structurechooser.html">Structure Chooser</a> interface is opened with options for manual association of PDB structures.</li>
+                       </ul> 
+                       </li>
+               <li>Choose the structure to view from the discovered list. This can be done either manually by clicking directly
+                       on the desired structure(s) in the list, or automatically by
+                       using the drop-down menu on the interface to filter and auto-select the best structure based on certain
+                       criteria like quality, resolution, etc.</li>
+               <li>When the desired structure(s) have been selected, they can be
+                       viewed by clicking the <strong>"View"</strong> button below the summary list.
+               </li> 
+
+       </ol>
+
        The
        <a href="jmol.html">Jmol viewer</a> has been included since Jalview
        2.3. Jalview 2.8.2 included support for <a href="chimera.html">Chimera</a>, provided it is
@@ -42,7 +59,8 @@
                        href="xsspannotation.html">Annotation from Structure</a> page for
                more information.
        </p>
-       <p>The following menu entries are provided for viewing structure data<br>
+       <!-- 
+       <p>The following menu entries are provided for viewing structure data
   <ul>
     <li>The <strong>&quot;Structure&#8594;View
         Structure&#8594;</strong> submenu allows a single PDB structure to be chosen
@@ -61,9 +79,9 @@
     <em>The View representative structures option was introduced in
         Jalview 2.8.1</em></li>
   </ul>
-</p>
+</p>  -->
 
-<p>If a single pdb
+<p>If a <strong>single</strong> pdb
 structure is selected, one of the following will happen:</p>
 
 <ul>
@@ -82,25 +100,7 @@ structure is selected, one of the following will happen:</p>
        <li style="list-style: none">See the <a href="jmol.html">Jmol
        </a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for more information about the display.</li>
 </ul>
-       <p><strong>Associating PDB files with Sequences</strong></p>
-       <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>
 
-<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 will also be saved in the <a
-               href="jalarchive.html">Jalview Archive file</a>.<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 the sequence's ID to query WSDBFetch, provided by the
-       EBI, and any enabled DAS servers, to discover PDB ids associated with the sequence.</li>
-</ul>
 
 <p><strong>Importing PDB Entries or files in PDB format</strong><br>
 You can retrieve sequences from the PDB using the <a

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 6bb2e3a..f84922e 100755 (executable)
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -24,138 +24,158 @@
 </head>
 
 <body>
-<p><strong>Popup Menu</strong><br>
-<em>This menu is visible when right clicking either within a
-selected region on the alignment or on a selected sequence name. It may
-not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
-<ul>
-  <li><strong>Selection</strong> 
-    <ul>
-      <li><a name="sqreport"><strong>Sequence Details...<br>
-          </strong></a><em>(Since Jalview 2.8)<br>Open an <a href="../io/exportseqreport.html">HTML report containing the annotation
-            and database cross references</a>&nbsp;normally shown in the sequence's
-            tooltip.</em></li>
-      <li><strong>Show Annotations...<br>
-          </strong><em>Choose to show (unhide) either All or 
-          a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
-      <li><strong>Hide Annotations...<br>
-          </strong><em>Choose to hide either All or 
-          a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
-      <li><a name="addrefannot"><strong>Add Reference Annotations<br>
-          </strong><em>Add to the alignment window any annotations on the selected sequences
-          which have been read from reference sources or calculated (for example, 
-          secondary structure derived from 3D structure). (Since Jalview 2.8.2)</em></li>
-      <li><strong>Edit </strong> 
-        <ul>
-          <li><strong>Copy</strong><br>
-            <em>Copies the selected region. In the applet version, the copied sequences 
-            are not available to the system clipboard.</em></li>
-          <li><strong>Cut<br>
-            </strong><em>Cuts the selected region from the alignment. In the applet 
-            version, the copied sequences are not available to the system clipboard.</em></li>
-          <li><strong>Edit Sequence</strong><br>
-            <em>Edit the selected sequence(s) directly. Spaces will be converted 
-            to the current gap character.</em></li>
-          <li><strong>To Upper Case</strong><em><strong><br>
-            </strong><em>Changes the case of selected region to lower case.</em> 
-            </em></li>
-          <li><strong>To Lower Case<br>
-            </strong><em>Changes the case of selected region to upper case.</em><strong> 
-            </strong></li>
-          <li><strong>Toggle Case</strong><br>
-            <em>Switches the case of all residues within the selected region.</em></li>
-        </ul>
-      </li>
-      <li><strong>Output to Textbox<br>
-        </strong><em>The selection area will be output to a a text window in the 
-        selected alignment format. </em></li>
-      <li><strong><a href="../features/creatinFeatures.html">Create Sequence Feature...</a></strong><br>
-        <em>Opens the dialog box for creating sequence features over the currently 
-        selected region on each selected sequence.</em></li>
-      <li><strong>Create Group<br>
-            </strong><em>This will define a new group from the current selection.</em><strong> 
-            </strong></li>
-          <li><strong>Remove Group<br>
-            </strong><em>This will undefine the selected group. </em><strong> 
-            </strong></li>
-          <li><strong>Edit (New) Group</strong><br>
-        <em>Group Editing Menu</em> <br />Options in this menu modify
-                                       the name and display properties of the currently selected group, or
-                                       a new group defined using the current selection.
+       <p>
+               <strong>Popup Menu</strong><br> <em>This menu is visible
+                       when right clicking either within a selected region on the alignment
+                       or on a selected sequence name. It may not be accessible when in
+                       'Cursor Mode' (toggled with the F2 key).</em>
+       </p>
+       <ul>
+               <li><strong>Selection</strong>
+                       <ul>
+                               <li><a name="sqreport"><strong>Sequence Details...<br>
+                                       </strong></a><em>(Since Jalview 2.8)<br>Open an <a
+                                               href="../io/exportseqreport.html">HTML report containing the
+                                                       annotation and database cross references</a>&nbsp;normally shown in
+                                               the sequence's tooltip.
+                               </em></li>
+                               <li><strong>Show Annotations...<br>
+                               </strong><em>Choose to show (unhide) either All or a selected type of
+                                               annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
+                               <li><strong>Hide Annotations...<br>
+                               </strong><em>Choose to hide either All or a selected type of annotation
+                                               for the selected sequences. (Since Jalview 2.8.2)</em></li>
+                               <li><a name="addrefannot"><strong>Add Reference
+                                                       Annotations<br>
+                                       </strong><em>Add to the alignment window any annotations on the
+                                                       selected sequences which have been read from reference sources or
+                                                       calculated (for example, secondary structure derived from 3D
+                                                       structure). (Since Jalview 2.8.2)</em></li>
+                               <li><strong>Edit </strong>
                                        <ul>
-          <li><strong>Name: &lt;Group&gt;</strong> or <strong>Edit name and description</strong><br><em>The first entry in the
-         menu displays the name for the currently selected group, if it has one. Selecting this option opens a window allowing the name and
-         description for this group to be edited. Click OK to set the
-         new name and decription, and cancel to leave the existing
-         name and description unchanged.</em></li>
-          <li><strong>Group Colour<br>
-            </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a> 
-            of the group.</em><strong> </strong></li>
-          <li><strong>Boxes<br>
-            </strong><em>If selected the background of a residue within the selected 
-            group will be coloured according to the assigned colour scheme.</em><strong> 
-            </strong></li>
-          <li><strong>Text<br>
-            </strong><em>If selected the selected group will display text. </em></li>
-          <li><strong>Colour Text<br>
-            </strong><em>If selected the selected group will display text in a 
-            colour slightly darker than the background colour of that residue.</em></li>
-          <li><strong>Border Colour <br>
-            </strong><em>Selecting this will display a &quot;Colour Chooser&quot; 
-            window. Select a colour than press OK to set the border colour of 
-            a group.</em></li>
-       <li><strong>Show Unconserved<br>
-         </strong><em>When this is selected, all symbols in the group matching the consensus sequence at that column will be rendered as a '.', highlighting mutations in the group area.
-       </em></li>
-                   </ul>
-      </li>
-<!-- not available in 2.5 yet
-    <li><strong>Group Links<br>
-    </strong><em>This menu is only visible if there are group links available for the current selection.
-    </em> 
-    <ul>
-    <li><em>ID links</em> allow you to send IDs associated with the current selection to a web server.</li>
-    <li><em>Sequence links</em> allow you to send the sequences in the currently selected region to a web server.</li>
-    <li><em>Sequence and ID links</em> allow you to send sets of IDs and sequences associated with the current selection to a web server.</li>
-    </ul>
-    <em>Group Links were added in Jalview 2.5</em></li>
--->    </ul>
-  </li>
-  <li><strong>Sequence Id<br>
-    </strong><em>This menu is only visible if you right-click on a sequence name. 
-    </em> 
-    <ul>
-      <li><a name="sqreport"><strong>Sequence Details ...<br>
-                                       </strong></a><em>(Since Jalview 2.8)<br>Open an <a href="../io/exportseqreport.html">HTML report containing the annotation
-                                               and database cross references</a> normally shown in the sequence's
-                                               tooltip.</em></li>
-                       <li><strong>Edit Name/Description<br>
-        </strong><em>You may edit the name and description of each sequence. A 
-        window will be displayed asking for a new sequence name and sequence description 
-        to be entered. Press OK to accept your edit. To save sequence descriptions, 
-        you must save in Fasta, PIR or Jalview File format.</em></li>
-      <li><a href="sqaddrefannot"><strong>Add Reference Annotations<br></strong><em>When enabled, copies any available alignment annotation for this sequence to the current view.</em></li>
-      <li><strong>Represent Group With (Sequence Id)</strong><br>
-        <em>All sequences in the current selection group will be hidden, apart 
-        from (Sequence Id). Any edits performed on the visible representative 
-        sequence will be propagated to the hidden sequences. </em></li>
-      <li><a name="sqid.popup"><strong>Link</strong><br>
-        <em>This menu item lists all links which have been set up in the <a href="../features/preferences.html">Preferences</a> 
-        Connections tab.<br>
-        Since Jalview 2.4, links will also be made for database cross 
-        references (where the database name exactly matches the link name set up in <a href="../features/preferences.html">Preferences</a>).
-        <br>Since Jalview 2.5, links are also shown for non-positional sequence features attached to 
-        the sequence, and any regular-expression based URL links that 
-        matched the description line.
-        </em><strong><br>
-        </strong></li>
-    </ul>
-  </li>
-  <li><strong>Structure</strong> 
-    </strong><em>This menu is only visible if you right-click on a sequence name. 
-    </em> 
-    <ul>
-      <li><strong>Associate Structure with Sequence</strong> 
+                                               <li><strong>Copy</strong><br> <em>Copies the
+                                                               selected region. In the applet version, the copied sequences are
+                                                               not available to the system clipboard.</em></li>
+                                               <li><strong>Cut<br>
+                                               </strong><em>Cuts the selected region from the alignment. In the
+                                                               applet version, the copied sequences are not available to the
+                                                               system clipboard.</em></li>
+                                               <li><strong>Edit Sequence</strong><br> <em>Edit the
+                                                               selected sequence(s) directly. Spaces will be converted to the
+                                                               current gap character.</em></li>
+                                               <li><strong>To Upper Case</strong><em><strong><br>
+                                                       </strong><em>Changes the case of selected region to lower case.</em> </em></li>
+                                               <li><strong>To Lower Case<br>
+                                               </strong><em>Changes the case of selected region to upper case.</em><strong>
+                                               </strong></li>
+                                               <li><strong>Toggle Case</strong><br> <em>Switches
+                                                               the case of all residues within the selected region.</em></li>
+                                       </ul></li>
+                               <li><strong>Output to Textbox<br>
+                               </strong><em>The selection area will be output to a a text window in the
+                                               selected alignment format. </em></li>
+                               <li><strong><a href="../features/creatinFeatures.html">Create
+                                                       Sequence Feature...</a></strong><br> <em>Opens the dialog box for
+                                               creating sequence features over the currently selected region on
+                                               each selected sequence.</em></li>
+                               <li><strong>Create Group<br>
+                               </strong><em>This will define a new group from the current selection.</em><strong>
+                               </strong></li>
+                               <li><strong>Remove Group<br>
+                               </strong><em>This will undefine the selected group. </em><strong> </strong></li>
+                               <li><strong>Edit (New) Group</strong><br> <em>Group
+                                               Editing Menu</em> <br />Options in this menu modify the name and
+                                       display properties of the currently selected group, or a new group
+                                       defined using the current selection.
+                                       <ul>
+                                               <li><strong>Name: &lt;Group&gt;</strong> or <strong>Edit
+                                                               name and description</strong><br> <em>The first entry in the
+                                                               menu displays the name for the currently selected group, if it
+                                                               has one. Selecting this option opens a window allowing the name
+                                                               and description for this group to be edited. Click OK to set the
+                                                               new name and decription, and cancel to leave the existing name
+                                                               and description unchanged.</em></li>
+                                               <li><strong>Group Colour<br>
+                                               </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a>
+                                                               of the group.
+                                               </em><strong> </strong></li>
+                                               <li><strong>Boxes<br>
+                                               </strong><em>If selected the background of a residue within the
+                                                               selected group will be coloured according to the assigned colour
+                                                               scheme.</em><strong> </strong></li>
+                                               <li><strong>Text<br>
+                                               </strong><em>If selected the selected group will display text. </em></li>
+                                               <li><strong>Colour Text<br>
+                                               </strong><em>If selected the selected group will display text in a
+                                                               colour slightly darker than the background colour of that
+                                                               residue.</em></li>
+                                               <li><strong>Border Colour <br>
+                                               </strong><em>Selecting this will display a &quot;Colour Chooser&quot;
+                                                               window. Select a colour than press OK to set the border colour
+                                                               of a group.</em></li>
+                                               <li><strong>Show Unconserved<br>
+                                               </strong><em>When this is selected, all symbols in the group matching
+                                                               the consensus sequence at that column will be rendered as a '.',
+                                                               highlighting mutations in the group area. </em></li>
+                                       </ul></li>
+
+                       </ul></li>
+               <li><strong>Sequence Id<br>
+               </strong><em>This menu is only visible if you right-click on a sequence
+                               name. </em>
+                       <ul>
+                               <li><a name="sqreport"><strong>Sequence Details
+                                                       ...<br>
+                                       </strong></a><em>(Since Jalview 2.8)<br>Open an <a
+                                               href="../io/exportseqreport.html">HTML report containing the
+                                                       annotation and database cross references</a> normally shown in the
+                                               sequence's tooltip.
+                               </em></li>
+                               <li><strong>Edit Name/Description<br>
+                               </strong><em>You may edit the name and description of each sequence. A
+                                               window will be displayed asking for a new sequence name and
+                                               sequence description to be entered. Press OK to accept your edit.
+                                               To save sequence descriptions, you must save in Fasta, PIR or
+                                               Jalview File format.</em></li>
+                               <li><a href="sqaddrefannot"><strong>Add Reference
+                                                       Annotations<br>
+                                       </strong><em>When enabled, copies any available alignment annotation
+                                                       for this sequence to the current view.</em></li>
+                               <li><strong>Represent Group With (Sequence Id)</strong><br>
+                                       <em>All sequences in the current selection group will be
+                                               hidden, apart from (Sequence Id). Any edits performed on the
+                                               visible representative sequence will be propagated to the hidden
+                                               sequences. </em></li>
+                               <li><a name="sqid.popup"><strong>Link</strong><br> <em>This
+                                                       menu item lists all links which have been set up in the <a
+                                                       href="../features/preferences.html">Preferences</a> Connections
+                                                       tab.<br> Since Jalview 2.4, links will also be made for
+                                                       database cross references (where the database name exactly
+                                                       matches the link name set up in <a
+                                                       href="../features/preferences.html">Preferences</a>). <br>Since
+                                                       Jalview 2.5, links are also shown for non-positional sequence
+                                                       features attached to the sequence, and any regular-expression
+                                                       based URL links that matched the description line.
+                                       </em><strong><br> </strong></li>
+                       </ul></li>
+               <li><strong>View Structure</strong> </strong><em>This menu is only
+                               visible if you right-click on a sequence name. If the
+                               sequence has an associated PDB file(s), Jalview will open a 'Structure Chooser' 
+                               dialogue with options to select the structure which will eventually be opened in
+                               a 3D interactive view.<br> These entries will only be present if the sequence
+                               has <a href="../features/viewingpdbs.html">associated PDB
+                                       structures</a>.<br /> If the sequence or alignment has RNA structure,
+                               then <strong>2D RNA</strong> entries will also be present enabling
+                               you to open a linked view of the RNA structure in <a
+                               href="../features/varna.html">VARNA</a>.
+               </em>
+               </li>
+<!-- 
+                       <p>
+                               <em>Other menu entries may also be shown if the current
+                                       selection includes sequences with associated structure data:</em><br>
+                       <ul>
+                               <li><strong>Associate Structure with Sequence</strong> 
         <ul>
           <li><strong>From File<br>
             </strong><em>Load a PDB file from local disk which will be associated 
@@ -172,37 +192,28 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
             alignment if the sequences have valid Uniprot names or accession ids. 
             </em></li>
         </ul>
-      </li>
-      <li><strong>View Structure<br>
-        </strong><em> If the sequence has an associated PDB file added by one 
-        of the methods described above, Jalview will open a 3D interactive 
-        view of the file.<br>
-        These entries will only be present if the sequence has <a
-                       href="../features/viewingpdbs.html">associated PDB structures</a>.<br/>
-                       If the sequence or alignment has RNA structure, then <strong>2D RNA</strong> entries will also be present enabling you to open a linked view of the RNA structure in <a href="../features/varna.html">VARNA</a>.</em><br>
-      </li>
-      <p><em>Other menu entries may also be shown if the current selection includes sequences with associated structure data:</em><br>
-  <ul>
-    <li><strong>&quot;Structure&#8594;View all <em>N</em>
-        structures<br/>
-    </strong><em>Opens a new window containing all structures associated
-      with the current selection, superposed according to the currently selected region of the alignment.<br/>(This
-      capability was added in Jalview 2.7)</em>
-    </li>
-    <li><strong>&quot;Structure&#8594;View all <em>N</em>
-        representative structures<br/>
-    </strong><em>Open a new window containing exactly one structure per
-      currently selected sequence.<br />
-    (The View representative structures option was introduced in
-        Jalview 2.8.1)</em></li>
-  </ul>
-  <br> 
-    </ul>
-  </li>
-  <li><strong>Hide Sequences</strong><br>
-    <em>Hides the currently selected sequences in this alignment view.</em><strong><br>
-    <br>
-    </strong></li>
-</ul>
+      </li> 
+
+                               <ul>
+                                       <li><strong>Structure&#8594;View all <em>N</em>
+                                                       structures<br />
+                                       </strong><em>Opens a new window containing all structures associated
+                                                       with the current selection, superposed according to the currently
+                                                       selected region of the alignment.<br />(This capability was
+                                                       added in Jalview 2.7)
+                                       </em></li>
+                                       <li><strong>Structure&#8594;View all <em>N</em>
+                                                       representative structures<br />
+                                       </strong><em>Open a new window containing exactly one structure per
+                                                       currently selected sequence.<br /> (The View representative
+                                                       structures option was introduced in Jalview 2.8.1)
+                                       </em></li>
+                               </ul>
+                               <br> -->
+                       
+               <li><strong>Hide Sequences</strong><br> <em>Hides the
+                               currently selected sequences in this alignment view.</em><strong><br>
+                               </strong></li>
+       </ul>
 </body>
 </html>