</tocitem>
<tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
<tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
- <tocitem text="PDB Structure Chooser" target="pdbchooser" />
+ <tocitem text="PDB & 3D-Beacons Structure Chooser" target="pdbchooser" />
<tocitem text="Jmol Viewer" target="pdbjmol" />
<tocitem text="Chimera Viewer" target="chimera" />
</tocitem>
the database you want to retrieve sequences</strong> from the database
chooser.
</p>
- <img src="selectfetchdb.gif" align="left" width="480" height="204"
+ <img src="selectfetchdb.gif" align="left"
alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
<p>
The databases are shown as a tree, and ordered alphabetically;
accession ids</strong> (as a semi-colon separated list), or press the
"Example" button to paste the example accession for the
currently selected database into the retrieval box. Finally, press
- "OK" to initiate the retrieval.</li>
+ "OK" to initiate the retrieval.
+ <br />
+ For the PDB and UniProt sequence fetchers, choose the "Retrieve IDs" tab
+ to search for accession ids.</li>
</ol>
<p>If you use the Sequence Fetcher, please remember to cite the
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>
</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
+ structure data, the 'PDBe 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
<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.
+ UniProt references might not always be found in which case you can revert to the PDB
+ search.
+ <br/>
+ <img src="3dbeacons_structurechooser.png"/>
+ <br/>
+ If structures are found through the 3D-Beacons network you can filter which structures
+ are shown using the drop-down filter at the top of the Structure Chooser window.
+ <br/>
+ You can view information about each related model, such as the resource providing
+ each model, in the columns displayed. You can sort the list of models 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
2.9. </em>
</p>
</body>
-</html>
\ No newline at end of file
+</html>
</head>
<body>
<p>
- <strong>Discovering and Viewing PDB Structures</strong>
+ <strong>Discovering and Viewing PDB and 3D-Beacons structures</strong>
</p>
Jalview can be used to explore the 3D structures of sequences in an
alignment by following the steps below:
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
+ <li>If one or more structures exist in the PDB for the given
sequence, the <a href="structurechooser.html">Structure
Chooser</a> dialog will open with them listed in the results
pane.
href="structurechooser.html">Structure Chooser</a> interface
will present options for manual association of PDB structures.
</li>
+ <li>
+ Since Jalview 2.11.2 you can also search the 3D-Beacons Network
+ for structures. The 3D-Beacons Network acts as a one-stop shop for protein
+ structures by combining and standardising data from several providers.
+ See <a href="structurechooser.html#3dbeaconssearch">3D-Beacons Search</a> for
+ instructions.
+ </li>
</ul>
</li>
- <li><strong>Selecting Structures</strong><br />You can select
+ <li><strong>Selecting PDB Structures</strong><br />
+ If one or more structures have been found from the PDB, 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
<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
+ provided it is installed and can be launched by Jalview. ChimeraX and PyMOL
+ support is included from Jalview 2.11.2. The default
viewer can be configured in the <a href="preferences.html#structure">Structure
tab</a> in the <strong>Tools→Preferences</strong> dialog box.
for more information.
</p>
<p>
- <img src="schooser_viewbutton.png"
- style="width: 465px; height: 81px" /><br/> <strong><a
+ <strong><a
name="afterviewbutton">Controlling where the new structures
will be shown</a></strong>
+ <br/>
+ <img src="schooser_viewbutton.png" />
<br />The Structure Chooser offers several options
- for viewing a structure. <br/><strong>New View</strong> will open a new
+ for viewing a structure. <br/>
+ The <strong>Open new structure view</strong> button 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
git://source.jalview.org / jalview.git / commitdiff
