- </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>
- <ul>
- <li><strong>From File<br>
- </strong><em>Load a PDB file from local disk which will be associated
- with this sequence. This file will be used if the user subsequently
- clicks on "View PDB Structure" menu item.</em></li>
- <li><strong>Enter PDB id<br>
- </strong><em>Enter the PDB id from an input window. This PDB id will
- be used by the service WSDBFetch, provided by the EBI, to fetch the
- PDB file if the user subsequently clicks on "View PDB Structure"
- menu item. </em></li>
- <li><strong>Discover PDB ids<br>
- </strong><em>This will use the service WSDBFetch, provided by the
- EBI, to retrieve all PDB ids associated with the sequences in the
- 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 display a 3D interactive
- viewer of the file.<br>
- These entries will only be present if the sequence has <a
- href="../features/viewingpdbs.html">associated PDB structures</a>.</em><br>
- </li>
- </ul>
- </li>
- <li><strong>Hide Sequences</strong><br>
- <em>Hides the currently selected sequences in this alignment view.</em><strong><br>
- <br>
+ <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: <Group></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 "Colour
+ Chooser" 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><strong>Add <a href="../features/annotation.html#seqannots">Reference Annotations</a></strong><br>
+ <em>When enabled, copies any available alignment
+ annotation for this sequence to the current view.</em></li>
+ <li><strong>Set as Reference</strong> or <strong>Unmark
+ as Reference</strong><br /> Sets or unsets the reference sequence for
+ the the alignment.</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>3D Structure Data...</strong> </strong><em>This menu is
+ visible when you right-click on a sequence name. When this
+ option is clicked, Jalview will open the <a
+ href="../features/structurechooser.html">'Structure
+ Chooser' </a>, which allows you to discover and view 3D structures
+ for the current selection. For more info, see <a
+ href="../features/viewingpdbs.html">viewing PDB structures</a>.
+ </em></li>
+ <li><strong>VARNA 2D Structure</strong><br />
+ <em> If the sequence or alignment has RNA structure, then <strong>VARNA
+ 2D Structure</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>
+ <li><a name="hideinserts"><strong>Hide Insertions</strong></a><br />
+ <em>Hides columns containing gaps in the current sequence or
+ selected region, and reveals columns not including gaps.</em>
+ <li><strong>Hide Sequences</strong><br> <em>Hides the
+ currently selected sequences in this alignment view.</em><strong><br>