JAL-3746 Updated help docs for 3D-Beacons. Added and altered images and text.

[jalview.git] / help / help / html / features / structurechooser.html

diff --git a/help/help/html/features/structurechooser.html b/help/help/html/features/structurechooser.html
index 785c429..11cad6b 100644 (file)
--- a/help/help/html/features/structurechooser.html
+++ b/help/help/html/features/structurechooser.html
@@ -32,8 +32,11 @@
     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>
@@ -69,6 +72,9 @@
     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>
@@ -86,7 +92,7 @@
   </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
@@ -103,7 +109,39 @@
     <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&mdash;which searches
+    across experimentally determined and predicted structure models from
+    several resources including PDBe, AlphaFold DB, SWISS-MODEL, PED, SASDB, Genome3D and
+    PDBe-KB&mdash;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
@@ -135,4 +173,4 @@
       2.9. </em>
   </p>
 </body>
-</html>
\ No newline at end of file
+</html>