</head>
<body>
- <p>
- <strong>Structure Chooser</strong>
- </p>
+ <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>"View Structure"</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>
+ <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>
-
- <strong>Associating PDB files with Sequences</strong><br>
- Discovery/Association of PDB entries to a sequence 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 <strong>'Configure Displayed Columns'</strong> 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 <strong>'Invert'</strong> 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; ">
+ <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>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>
+ <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>
+ <p>
+ <em>The Structure Chooser interface was introduced in Jalview
+ 2.9. </em>
+ </p>
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