- <li><a name="viewreps"/>The <strong>"Structure→View all <em>N</em>
- representative structures
- </strong> option will open a new window containing exactly one structure per
- currently selected sequence.<br />
- <em>The View representative structures option was introduced in
- Jalview 2.8.1</em></li>
- </ul>
- <br>
-</p>
-
-<p>If a single pdb
-structure is selected, one of the following will happen:</p>
-
-<ul>
- <li>If no structures are open, then an interactive display of the
- structure will be opened in a new window</li>
-
- <li>If another structure is already shown for the current
- alignment, then you will be asked if you want to add and <a
- href="jmol.html#align">align this structure</a> to the structure in
- the existing view. (<em>new feature in Jalview 2.6</em>)</li>
-
- <li>If the structure is already shown, then you will be prompted
- to associate the sequence with an existing view of the selected
- structure. This is useful when working with multi-domain or multi-chain PDB files.</li>
-
- <li style="list-style: none">See the <a href="jmol.html">Jmol
- PDB viewer</a> help page 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>→</strong> Associate Structure with
-Sequence", and one of the submenus:</p>
+ <li><strong>Selecting Structures</strong><br />You can select
+ the structures that you want to open and view by selecting them
+ with the mouse and keyboard.<br />By default, if structures were
+ discovered, then some will already be selected according to the
+ criteria shown in the drop-down menu. The default criteria is
+ 'highest resolution', simply choose another to pick structures in
+ a different way.<br />
+ <ul>
+ <li><strong>Viewing Cached Structures</strong><br />If
+ previously downloaded structures are available for your
+ sequences, the structure chooser will automatically offer them
+ via the <strong>Cached Structures</strong> view. If you wish
+ to download new structures, select one of the PDBe selection
+ criteria from the drop-down menu.</li>
+ </ul></li>
+ <li><strong>To view selected structures, click the <strong>"View"</strong>
+ button.
+ </strong><br />
+ <ul>
+ <li>Additional structure data will be downloaded with the
+ EMBL-EBI's dbfetch service</li>
+ <li><a href="siftsmapping.html">SIFTS</a> records will also
+ be downloaded for mapping UniProt protein sequence data to PDB
+ coordinates.</li>
+ <li>A new structure viewer will open, or you will be
+ prompted to add structures to existing viewers (see <a
+ href="#afterviewbutton">below</a> for details).
+ </li>
+ </ul></li>
+ </ol>
+ <p>
+ <strong>Structure Viewers in the Jalview Desktop</strong><br /> 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 installed and can be launched by Jalview. The default
+ viewer can be configured in the <a href="preferences.html#structure">Structure
+ tab</a> in the <strong>Tools→Preferences</strong> dialog box.
+
+ <p>
+ Structure data imported into Jalview can also be processed to
+ display secondary structure and temperature factor annotation. See
+ the <a href="xsspannotation.html">Annotation from Structure</a> page
+ for more information.
+ </p>
+ <p>
+ <img src="schooser_viewbutton.png"
+ style="width: 465px; height: 81px" /><br/> <strong><a
+ name="afterviewbutton">Controlling where the new structures
+ will be shown</a></strong>
+ <br />The Structure Chooser offers several options
+ for viewing a structure. <br/><strong>New View</strong> will open a new
+ structure viewer for the selected structures, but if there are views
+ already open, you can select which one to use, and press the <strong>Add</strong>
+ button. Jalview can automatically superimpose new structures based
+ on the linked alignments - but if this is not desirable, simple
+ un-tick the <strong>Superpose Structures</strong> checkbox.