--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Structure Chooser</title>
+</head>
+
+<body>
+ <p>
+ <strong>Structure Chooser Dialog Box</strong>
+ </p>
+
+ <p>
+ 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
+ provides:
+ </p>
+ <ul>
+ <li>Automatic discovery, retrieval and association of PDB
+ entries for sequences</li>
+ <li>Exploration of meta-data for available 3D structures</li>
+ <li>Automatic selection of the 'best structure' to display for
+ each sequence</li>
+ <li>Manual association of PDB entries by entering a PDB Id</li>
+ <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>The drop-down menu offers different options for structure
+ discovery; the 'Cached' view is shown automatically if existing
+ structure data has been imported for the selected sequences, and if
+ none is available, the import PDB/mmCIF file options are shown.</p>
+ <p>
+ Once one or more structures have been selected, pressing the <strong>View</strong>
+ or <strong>Add</strong> button will import them <a
+ href="viewingpdbs.html#afterviewbutton">a new or existing
+ structure view</a>. When multiple views are available, use the
+ drop-down menu to pick the target viewer for the structures.
+ </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
+ associated with the sequence. It does this based on the sequence's
+ ID string, and any other associated database IDs. <br />
+ <br />
+ <p>
+ <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>
+ <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
+ 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;">
+ <!-- <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; ">
+ <p><img src="schooser_from-file.png" style="width: 468px; height: 370px; ">
+ <p><img src="schooser_cached.png"> -->
+ <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>
+ <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: 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:
+ <ul>
+ <li><strong>From File</strong> - allows you to load a PDB file
+ from the local machine or network and associate it with the
+ selected sequence. PDB files associated in this way will also be
+ saved in the <a href="jalarchive.html">Jalview Archive file</a>.<br></li>
+ <li><strong>Enter PDB Id</strong> - allows you specify a PDB ID
+ for your sequence. The PDB Rest API, provided by EMBL-EBI, is used
+ to validate and fetch structure data.<br></li>
+ </ul>
+
+ <p>
+ <em>The Structure Chooser interface was introduced in Jalview
+ 2.9. </em>
+ </p>
+</body>
+</html>
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