<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
'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 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.
<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>
+ <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.
+ </p>
<p>
- If a <strong>single</strong> PDB structure is selected, one of the
- following will happen:
+ <em>Superposing structures</em><br/>Jalview superposes structures using
+ the visible portions of any associated sequence alignments. A
+ message in the structure viewer's status bar will be shown if not
+ enough aligned columns were available to perform a superposition.
</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
- </a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for
- more information about the display.
- </li>
- </ul>
-
+ <p>
+ See the <a href="jmol.html">Jmol
+ </a> and <a href="chimera.html">Chimera</a> help pages for
+ more information about their capabilities.</p>
+
<p>
<strong>Retrieving sequences from the PDB</strong><br>You can
git://source.jalview.org / jalview.git / blobdiff