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<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
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<body>
- <p>
- <strong>Structure Chooser</strong>
- </p>
+ <p>
+ <strong>Structure Chooser</strong>
+ </p>
- The Structure Chooser panel was added in Jalview 2.8.3. It
- introduced a smarter technique for selecting PDB structures to view in
- Jalview by quering readily available meta-data of the structures. Some of the main features it provides are listed below:
- <ul>
- <li>Automatic discovery, retrieval and association of PDB entries
- for an alignment's sequences</li>
- <li>Visualisation of discovered structures' meta-data</li>
- <li>Ability to configure the meta-data entries to visualise</li>
- <li>Auto-selection of the best structure via filtering by
- the available metric parameters in the meta-data (i.e. resolution,
- quality etc).</li>
- <li>Selection of multiple structures in a single operation</li>
- </ul>
- Additionally, the Structure Chooser retains the following contemporary
- feature of Jalview:
- <ul>
- <li>Manual association of PDB entries via entering the PDB Id or
- From File</li>
- <li>Ability to view cached PDB entries</li>
- </ul>
+ <p>
+ The Structure Chooser interface allows you to interactively select
+ which PDB 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>
+ 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
+ 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>
- <p><img src="schooser_main.png" style="width: 464px; height: 369px; ">
- <!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
+ <img src="schooser_main.png" style="width: 464px; height: 369px;">
+ <!-- <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>
-
- <strong>Auto-Selection of Structures</strong>
-
+ <br>The screenshot above shows the Structure Chooser interface
+ along with the meta-data of auto-discovered structures for the
+ 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;">
+ <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>
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