<html>
<!--
- * 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)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
</head>
<body>
- <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><img src="schooser_main.png" style="width: 464px; height: 369px; ">
- <!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
+ <p>
+ <strong>Structure Chooser</strong>
+ </p>
+
+ The Structure Chooser interface provides a smart technique for
+ selecting PDB structures to view in Jalview by querying readily
+ available meta-data of structures. The Interface can be invoked by
+ selecting the
+ <strong>"3D Structure Data.."</strong> option from a sequence's
+ <a href="../menus/popupMenu.html">pop-up menu</a>. 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
+ features 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>
+
+
+ <strong>Associating PDB files with Sequences</strong>
+ <br> Discovery/Association of PDB entries to a sequence now
+ happens automatically during the initialisation of the Structure
+ Chooser Interface. Jalview uses the sequence's ID to query the PDB
+ Rest API provided by the EBI to discover PDB Ids associated with the
+ sequence.
+
+ <br>
+ <br>
+ <strong>Configuring displayed meta-data for Structures</strong>
+ <br> To configure the visible meta-data displayed for the
+ discovered structures, click the 'Configure Displayed Columns' tab,
+ then tick the options which you intend to make visible.
+
+ <br>
+ <br>
+ <strong>Auto-selection of best Structures</strong>
+ <br> Jalview can automatically filter and select the best
+ structures using various metric categories avaialble from the
+ meta-data of the structures. To perform this simply select any of the
+ following options from the drop-down menu in the Structure Chooser
+ interface: Best Uniprot coverage, Higest Resolution, Best Quality,
+ Highest Protein Chain etc. When the 'Invert' option is selected,
+ Jalview returns an inverse result for the current selected option in
+ the drop-down menu.
+ <p>
+
+ <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. Note however that if no structures were
+ auto-discovered, a different interface for manual association will
+ be invoked as seen in the screenshot below.
+ <p>
+ <img src="schooser_enter-id.png"
+ style="width: 464px; height: 369px;"
+ >
+ <p>
+ <strong>Manual selection/association of PDB files with
+ Sequences</strong>
+ </p>
+ <p>To manually associate PDB files with a sequence, select any of
+ the follwing options listed below from the drop-down menu in the
+ interface:
+ <ul>
+ <li><strong>From File</strong> - You can 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> - Jalview will use the PDB
+ Rest API, provided by the EBI, to fetch the PDB file with the
+ entered Id.<br></li>
+ <li><strong>Cached PDB Entries</strong> - You can view PDB
+ structures which have previously been downloaded/viewed using this
+ option. Jalview caches previously downloaded PDB entries in the
+ computer memory. However, if the project is saved before exiting
+ Jalview, Jalview will serialize the cached entries to the file
+ system.</li>
+ </ul>
+
+ <p>
+ <em>The Structure Chooser interface was introduced in Jalview
+ 2.9. </em>
+ </p>
</body>
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