<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
Jalview can be used to view protein structures by following the steps below:
<ol>
<li>Select the <strong>"View Structure"</strong> option from a
- sequence's <a href="../menus/popupMenu.html">pop-up menu</a>.
+ sequence's <a href="../menus/popupMenu.html">pop-up menu</a> to invoke the <a href="structurechooser.html">Structure Chooser</a> interface.
<ul>
- <li>If one or more structures exists for the given sequence, the <strong>'Structure Chooser'</strong>
+ <li>If one or more structures exists for the given sequence, the <a href="structurechooser.html">Structure Chooser</a>
dialogue is opened with a list of the found structures meta-data.</li>
- <li>However, if no structure was found, the <strong>'Structure Chooser'</strong> dialogue is opened with options for manual association of PDB structures.</li>
+ <li>However, if no structure was found, the <a href="structurechooser.html">Structure Chooser</a> interface is opened with options for manual association of PDB structures.</li>
</ul>
</li>
- <li>Choose the structure to view from the presented structures
- summary list. This can be done either manually by clicking directly
- on the desired structure from the list, or automatically by
- using the filter combo-box which enables filtering on certain
- criteria like quality, resolution, etc. The best structure for the chosen criteria is automatically selected by the filtration process. </li>
+ <li>Choose the structure to view from the discovered list. This can be done either manually by clicking directly
+ on the desired structure(s) in the list, or automatically by
+ using the drop-down menu on the interface to filter and auto-select the best structure based on certain
+ criteria like quality, resolution, etc.</li>
<li>When the desired structure(s) have been selected, they can be
viewed by clicking the <strong>"View"</strong> button below the summary list.
</li>
<li style="list-style: none">See the <a href="jmol.html">Jmol
</a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for more information about the display.</li>
</ul>
- <p><strong>Associating PDB files with Sequences</strong></p>
- <p>Since Jalview 2.8.3, discovery of PDB Id associated to a sequence happens automatically when the <strong>"View Structure"</strong> option is selected
- from a sequence's <a href="../menus/popupMenu.html">pop-up menu</a>. Jalview uses the sequence's ID to query the PDB Rest API, provided by the
- EBI to discover PDB ids associated with the sequence. </p>
-
- <p><strong>Manual association of PDB files with Sequences</strong> </p>
- <p>To manually associate PDB files with a sequence, right click on a sequence
-ID and select the <strong>"View Structure"</strong> option, this opens the <strong>'Structure Chooser'</strong> dialogue. Then pick any of the follwing options listed below from the drop-down menu in the <strong>'Structure Chooser'</strong> panel to proceed with manual association:
-<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>
-</ul>
-
-<strong>Note:</strong> The drop-down menu in the 'Structure Chooser' panel may contain other options employed for filtering structures when one or more structures are auto-discovered.
<p><strong>Importing PDB Entries or files in PDB format</strong><br>
You can retrieve sequences from the PDB using the <a
git://source.jalview.org / jalview.git / commitdiff
