Annotations<br>
</strong><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
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
- with this sequence. This file will be used if the user subsequently
- clicks on "View 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 its "View 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>
-
- <ul>
- <li><strong>Structure→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→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
+ <li><strong>Hide Insertions</strong><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>
</strong></li>
</ul>