<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:
+ 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,
+ <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:
+ 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><img src="schooser_main.png" style="width: 464px; height: 369px; ">
- <!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
+
+ <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; ">
<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 panel was introduced in Jalview 2.x.x.
+ </em>
+ </p>
</body>
</html>
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff