<title>PDB Viewing</title>
</head>
<body>
-<p><strong>Viewing PDB Structures</strong></p>
<p>
- Jalview can view protein structures associated with a sequence via the
- <strong>"Structure→"</strong> submenu from a sequence's <a
- href="../menus/popupMenu.html">pop-up menu</a>.
+ <strong>Viewing PDB Structures</strong>
</p>
+ 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>.
+ <ul>
+ <li>If one or more structures exists for the given sequence, the <strong>'Structure Chooser'</strong>
+ 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>
+ </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>When the desired structure(s) have been selected, they can be
+ viewed by clicking the <strong>"View"</strong> button below the summary list.
+ </li>
+
+ </ol>
+
The
<a href="jmol.html">Jmol viewer</a> has been included since Jalview
2.3. Jalview 2.8.2 included support for <a href="chimera.html">Chimera</a>, provided it is
href="xsspannotation.html">Annotation from Structure</a> page for
more information.
</p>
- <p>The following menu entries are provided for viewing structure data<br>
+ <!--
+ <p>The following menu entries are provided for viewing structure data
<ul>
<li>The <strong>"Structure→View
Structure→</strong> submenu allows a single PDB structure to be chosen
<em>The View representative structures option was introduced in
Jalview 2.8.1</em></li>
</ul>
-</p>
+</p> -->
-<p>If a single pdb
+<p>If a <strong>single</strong> pdb
structure is selected, one of the following will happen:</p>
<ul>
</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>To associate PDB files with a sequence, right click on a sequence
-ID and select "Structure<strong>→</strong> Associate Structure with
-Sequence", and one of the submenus:</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>From File - You can load a PDB file from the local machine or
+ <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>Enter PDB Id - Jalview will use WSDBFetch, provided by the
+ <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>Discover PDB Ids - Jalview uses the sequence's ID to query WSDBFetch, provided by the
- EBI, and any enabled DAS servers, to discover PDB ids associated with the sequence.</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
href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with
git://source.jalview.org / jalview.git / blobdiff