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 / blobdiff