- <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>
+ <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>
+ </li>
+ <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>
+ <strong><a name="afterviewbutton">After pressing the
+ 'View' button in the Structure Chooser</a></strong><br /> The behaviour of
+ the 'View' button depends on the number of structures selected, and
+ whether structure views already exist for the selected structures or
+ aligned sequences.
+ </p>
+ <p>If multiple structures are selected, then Jalview will always
+ create a new structure view. The selected structures will be
+ imported into this view, and superposed with the matched positions
+ from the aligned sequences. A message in the structure viewer's
+ status bar will be shown if not enough aligned columns were
+ available to perform a superposition.</p>
+ <p>
+ If a <strong>single</strong> PDB structure is selected, one of the
+ following will happen:
+ </p>