<p>
The Structure Chooser interface allows you to interactively select
which PDB structures to view for the currently selected set of
- sequences. It's opened by selecting the <strong>"3D
+ sequences. It is opened by selecting the <strong>"3D
Structure Data.."</strong> option from the Sequence ID panel's <a
href="../menus/popupMenu.html">pop-up menu</a>. The dialog
provides:
<li>Association of structure data from a local file (in mmCIF
or PDB format)</li>
</ul>
-
+ <p>
+ <strong>Selecting and Viewing Structures</strong>
+ </p>
+ <p>
+ Once one or more structures have been selected, pressing the <strong>View</strong>
+ button will import them into <a
+ href="viewingpdbs.html#afterviewbutton">a new or existing
+ structure view</a>.
+ </p>
<p>
<strong>Automated discovery of structure data</strong>
</p>
- <p>After selecting "3D Structure Data ..", Jalview queries the PDB
- via the PDBe SOLR Rest API provided by EMBL-EBI to discover PDB ids
+ <p>
+ After selecting "3D Structure Data ..", Jalview queries the PDB via
+ the PDBe SOLR Rest API provided by EMBL-EBI to discover PDB IDs
associated with the sequence. It does this based on the sequence's
- ID string, and any other associated database IDs.</p>
+ ID string, and any other associated database IDs. <br />
+ <br />
<p>
- <strong>Exploration of meta-data for available structures</strong>
+ <strong><a name="cachedstructview">Viewing existing
+ structures for your sequences</a></strong>
+ </p>
+ <p>
+ If you have already loaded 3D structure data for the selected
+ sequences, the structure chooser will first open with the <strong>Cached
+ Structures View</strong>. This view shows associations between each
+ sequence, and chains for 3D structure files already in memory. If
+ you want to download additional structures, select one of the other
+ options from the drop down menu.
</p>
- <p>Information on each structure available is displayed in columns
- in the dialog box. By default, only the title, resolution and PDB
- identifier are shown, but many more are provided by the PDBe. To
- configure which ones are displayed, select the 'Configure Displayed
- Columns' tab and tick the columns which you want to see.</p>
<p>
<strong>Selection of the best structure for each sequence</strong>
</p>
<p>Jalview can automatically select the best structures according
- to meta-data provided by the PDB. By default, the 'Best Quality'
- structure for each sequence will be selected, but clicking on the
- drop down menu allows other criteria to be chosen, including
- Resolution (only defined for X-Ray structures), Highest Protein
- Chain etc. When 'Invert' is selected, structures are selected in
- reverse order for the current criteria (e.g. worst quality rather
- than best).</p>
+ to meta-data provided by the PDB. For alignments with no existing
+ structure data, the 'Best Quality' structure for each sequence will
+ by default be selected, but clicking on the drop down menu allows
+ other criteria to be chosen, including Resolution (only defined for
+ X-Ray structures), Highest Protein Chain etc. When 'Invert' is
+ selected, structures are selected in reverse order for the current
+ criteria (e.g. worst quality rather than best).</p>
<p>
<img src="schooser_main.png" style="width: 464px; height: 369px;">
<p><img src="schooser_cached.png"> -->
<br>The screenshot above shows the Structure Chooser interface
along with the meta-data of auto-discovered structures for the
- sample alignment. Note however that if no structures were
- auto-discovered, a different interface for manual association will
- be invoked as seen in the screenshot below.
+ sample alignment. If no structures were
+ auto-discovered, options for manually associating PDB records will be shown (see below).
+ <p>
+ <strong>Exploration of meta-data for available structures</strong>
+ </p>
+ <p>Information on each structure available is displayed in columns
+ in the dialog box. By default, only the title, resolution and PDB
+ identifier are shown, but many more are provided by the PDBe. To
+ configure which ones are displayed, select the 'Configure Displayed
+ Columns' tab and tick the columns which you want to see.</p>
<p>
<img src="schooser_enter-id.png"
style="width: 464px; height: 369px;">
- <p>
+ <br/>
<strong>Manual selection/association of PDB files with
Sequences</strong>
</p>
for your sequence. The PDB Rest API, provided by EMBL-EBI, is used
to validate and fetch structure data.<br></li>
</ul>
- <p>
- <strong>Viewing existing structures for your sequences</strong>
- </p>
- <p>
- If you have previously associated structure data on the alignment,
- selecting <strong>Cached PDB Entries</strong> from the drop down
- menu allows you to select these structures for display.
- </p>
<p>
<em>The Structure Chooser interface was introduced in 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 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>
-
+ <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
the <a href="xsspannotation.html">Annotation from Structure</a> page
for more information.
</p>
-
<p>
- If a <strong>single</strong> PDB structure is selected, one of the
- following will happen:
+ <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.<br /> If a <strong>single</strong> PDB structure
+ is selected, one of the following will happen:
</p>
<ul>
<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>
+ 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
prompted to associate the sequence with an existing view of the
git://source.jalview.org / jalview.git / commitdiff