- <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>"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
- 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
- <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>Discovering and Viewing PDB Structures</strong>
+ </p>
+ Jalview can be used to explore the 3D structures of sequences in an
+ alignment 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>