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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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<head>
<title>PDB Viewing</title>
</head>
<body>
-<p><strong>Viewing PDB Structures</strong></p>
+ <p>
+ <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> to invoke the <a href="structurechooser.html">Structure Chooser</a> interface.
+ <ul>
+ <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 <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 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>
+
+ </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
+ installed and can be launched by Jalview. The default viewer can be
+ configured in the
+ <a href="preferences.html#structure">Structure tab</a> in the
+ <strong>Tools→Preferences</strong> dialog box.
+ <p>
+ Structure data imported into Jalview can also be processed to display
+ secondary structure and temperature factor annotation. See the <a
+ href="xsspannotation.html">Annotation from Structure</a> page for
+ more information.
+ </p>
+ <!--
+ <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
+ for display from the available structures for a sequence.
+ </li>
+ <li>The <strong>"Structure→View all <em>N</em>
+ structures
+ </strong> option will open a new window containing all structures associated
+ with the current selection, superposed according to the currently selected region of the alignment.<br/><em>This
+ capability was added in Jalview 2.7</em>
+ </li>
+ <li>The <strong>"Structure→View all <em>N</em>
+ representative structures
+ </strong> option will open a new window containing exactly one structure per
+ currently selected sequence.<br />
+ <em>The View representative structures option was introduced in
+ Jalview 2.8.1</em></li>
+ </ul>
+</p> -->
-<p>Jalview can view protein structures associated with a sequence
-via the <strong>"Structure→View PDB entry:"</strong> entries from a
-sequence's <a href="../menus/popupMenu.html">pop-up menu</a>. Once a pdb
+<p>If a <strong>single</strong> pdb
structure is selected, one of the following will happen:</p>
<ul>
<li>If no structures are open, then an interactive display of the
- structure will be opened in a new window</li>
+ structure will be opened in a new window.</li>
<li>If another structure is already shown for the current
alignment, then you will be asked if you want to add and <a
href="jmol.html#align">align this structure</a> to the structure in
- the existing view. (<em>new feature in Jalview 2.6</em>)</li>
+ the existing view. (<em>new feature in Jalview 2.6</em>).</li>
<li>If the structure is already shown, then you will be prompted
to associate the sequence with an existing view of the selected
structure. This is useful when working with multi-domain or multi-chain PDB files.</li>
<li style="list-style: none">See the <a href="jmol.html">Jmol
- PDB viewer</a> help page for more information about the display.</li>
+ </a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for more information about the display.</li>
</ul>
- <p>
- <em>Opening structures associated with the current selection</em><br />
- If one or more of the sequences in the alignment are selected, then
- the Structure submenu of the <a href="../menus/popupMenu.html">Sequence
- ID popup menu</a> will contain will include either a 'View all <em>X</em>
- structures' entry in the submenu or a 'View structure for <em>Sequence</em>'
- entry. Both these options will open a new Jmol view containing one, or
- all the structures available for all selected sequences, superimposed
- using the currently selected region of the alignment. (<em>This
- capability was added in Jalview 2.7</em>)
- </p>
- <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>
-
-<ul>
- <li>From File - 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
- 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>
<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