-<p><strong>Viewing PDB Structures</strong></p>
- <p>
- Jalview can view protein structures associated with a sequence via the
- <strong>"Structure→"</strong> submenu from a sequence's <a
- href="../menus/popupMenu.html">pop-up menu</a>.
- </p>
- 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>The following menu entries are provided for viewing structure data<br>
- <ul>
- <li>The <strong>"Structure→View
- Structure→</strong> submenu allows a single PDB structure to be chosen
- for display from the available structures for a sequence.
+ <p>
+ <strong>Viewing PDB Structures</strong>
+ </p>
+ Jalview can be used to view protein structures by following the steps
+ below:
+ <ol>
+ <li>Select the <strong>"3D Structure Data..."</strong> option
+ from a sequence's <a href="../menus/popupMenu.html">pop-up
+ menu</a> to open the <a href="structurechooser.html">Structure
+ Chooser</a> dialog box.
+ <ul>
+ <li>If one or more structures exists for the given
+ sequence, the <a href="structurechooser.html">Structure
+ Chooser</a> dialog will open with them listed in the results
+ pane.
+ </li>
+ <li>However, if no structure was found, the <a
+ href="structurechooser.html"
+ >Structure Chooser</a> interface will present options for manual
+ association of PDB structures.
+ </li>
+ </ul>