</head>
<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's 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><img src="schooser_main.png" style="width: 464px; height: 369px; ">
- <!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
+ <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.</p>
+ <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>
+ <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. By default, the 'Best Quality'
+ structure for each sequence will 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: 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 '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>
+ <strong>Viewing existing structures for your sequences</strong>
+ </p>
+ <p>
+ If you have previously associated structure data on the alignment,
+ selecting <strong>Cached PDB Entries</strong> from the drop down
+ menu allows you to select these structures for display.
+ </p>
+
+ <p>
+ <em>The Structure Chooser interface was introduced in Jalview
+ 2.9. </em>
+ </p>
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