The Structure Chooser allows you to select
3D structures to view for the currently selected set of
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
+ Structure Data..."</strong> option from the Sequence ID panel's
+ <a href="../menus/popupMenu.html">pop-up menu</a>. <br/>
+ <img src="3dstructuredata_popupmenu.png" alt="pop-up menu"/>
+ <br/>
+ The dialog
provides:
</p>
<ul>
associated with the sequence. It does this based on the sequence's
ID string, and any other associated database IDs. <br />
<br />
+ Since Jalview 2.11.2, you can also <a href="#3dbeaconssearch">initiate a search
+ of the 3D-Beacons Network</a>.
+ </p>
<p>
<strong><a name="cachedstructview">Viewing existing
structures for your sequences</a></strong>
<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. 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
+ to meta-data provided by the search service. The 'PDBe Best Quality' structure for each sequence will
+ by default be selected when no other structure data is available. If 3D-models from other sources are also available, then 'Best 3D Beacons coverage' will be show.
+ <br/><br/>Clicking on the drop down menu allows
+ other criteria to be chosen. For the PDBe, these include including Resolution (only defined for
+ X-Ray structures), Highest Protein Chain etc. When 3D-Beacons results are available, structures can be selected based on their specific provider, or by their coverage of the aligned sequences.<br/>
+ <br/>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: 499px; height: 437px;">
+ <img src="schooser_main.png" style="width: 820px; height: 458px;">
<!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
<p><img src="schooser_drop-down.png" style="width: 464px; height: 368px; ">
<p><img src="schooser_enter-id.png" style="width: 467px; height: 373px; ">
<br>The screenshot above shows the Structure Chooser displayed after
selecting all the sequences in the Jalview example project. If no
structures were auto-discovered, options for manually associating
- PDB records will be shown (see below).<p>
+ PDB records will be shown (see below).
+
+ <p>
+ <strong><a name="3dbeaconssearch">3D-Beacons Network Search</a></strong>
+ </p>
+ <p>
+ To initiate a search of the 3D-Beacons Network—which searches
+ across experimentally determined and predicted structure models from
+ several resources including PDBe, AlphaFold DB, SWISS-MODEL, PED, SASDB, Genome3D and
+ PDBe-KB—click on the <strong>3D-Beacons Search</strong> button at the top of the
+ Structure Chooser window.
+ <br/>
+ <img src="3dbeacons_button.png"/>
+ <br/>
+ The 3D-Beacons Network search requires UniProt references and Jalview will ask
+ to attempt to fetch these references for the selected sequences.
+ If no UniProt references are found, Jalview will still search the PDB for potential matches for the sequence's ID string.
+ <br/>
+ <img src="3dbeacons_structurechooser.png"/>
+ <br/>
+ Structures found through the 3D-Beacons network can be filtered using the drop-down filter at the top of the Structure Chooser window.
+ You can view information about each related model, such as the resource providing
+ each model, in the displayed columns, and models can be reordered by clicking on
+ column headings.
+ <br/>
+ Select and view the structures in the usual way using the <a href="viewingpdbs.html#afterviewbutton">open structure options</a> at
+ the bottom of the Structure Chooser window.
+ </p>
+
+ <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>
+ identifier are shown, but many more are provided by the PDBe.
+ 3D-Beacons structures have different data, including a quality score
+ (such as Qmeans_DISCO). 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: 173px;">
- <br/>
- <strong>Manual selection/association of PDB files with
- Sequences</strong>
+ style="width: 464px; height: 173px;"> <br /> <strong>Manual
+ selection/association of PDB files with Sequences</strong>
</p>
<p>To manually associate PDB files with a sequence, select 'From
File', or 'Enter PDB Id' from the drop-down menu:
2.9. </em>
</p>
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