<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:
+ <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 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>
+ 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>
- 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>
+ <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;">
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;"
- >
+ 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:
+ <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> - 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>
+ <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
git://source.jalview.org / jalview.git / commitdiff