'highest resolution', simply choose another to pick structures in
a different way.<br />
<ul>
- <li><strong>Viewing Cached Structures</strong><br />If you
- have previously downloaded structures for your sequences, they
- can be viewed by selecting the <strong>Cached PDB
- Entries</strong> option from the drop down menu at the top of the
- dialog box.</li>
+ <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 PDB Entries</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.
<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>
-
- 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>
+ <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:
<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>).
+ href="jmol.html#align"></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
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