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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
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-<head><title>PDB Viewing</title></head>
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<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→View
- PDB entry:"</strong> entries from a sequence's <a
- href="../menus/popupMenu.html">pop-up menu</a>. This will open an
- interactive display of the structure in a new window, or prompt you
- to associate the sequence with an existing view of the selected
- structure. See the <a href="jmol.html">Jmol PDB viewer</a> help page
- for more information about the display.
-</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>
+ <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>If a <strong>single</strong> pdb
+structure is selected, one of the following will happen:</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 WSDBFetch, provided by the EBI, to discover
- PDB ids for all the sequences in the alignment which have valid Uniprot names
- / accession ids. </li>
+ <li>If no structures are open, then an interactive display of the
+ 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>
+
+ <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
+ </a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for more information about the display.</li>
</ul>
+
+
<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 this
- service are automatically associated with their source database entry. For PDB
- sequences, simply select PDB as the database and enter your known PDB id (appended
- with ':' and a chain code, if desired).
-<br>Jalview will also read PDB files directly. Simply load in the file
-as you would an alignment file. The sequences of any peptide chains
-will be extracted from the file and viewed in the alignment window.
-<br><em>Note for jalview applet users: due to the applet security
-constraints, PDB Files can currently only be imported by cut and paste
-of the PDB file text into the text box opened by the 'From File' entry
-of the structure menu.</p>
+ href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with
+this service are automatically associated with their source database
+entry. For PDB sequences, simply select PDB as the database and enter
+your known PDB id (appended with ':' and a chain code, if desired).<br>
+Jalview will also read PDB files directly. Simply load in the file as
+you would an alignment file. The sequences of any peptide chains will be
+extracted from the file and viewed in the alignment window.</p>
+
+<p>
+<strong>Associating a large number of PDB files to sequences
+in an alignment</strong><br /> It is often the case when working with
+structure alignments that you will have a directory of PDB files, and
+an alignment involving one or more of the structures. If you drag a
+number of PDB files onto an alignment in the Jalview desktop, Jalview
+will give you the option of associating PDB files with sequences that
+have the same filename. This means, for example, you can automatically
+associate PDB files with names like '1gaq.pdb' with sequences that
+have an ID like '1gaq'.
+<br/><em>Note: This feature was added in Jalview 2.7</em>
+</p>
+<p><em>Note for Jalview applet users:<br>
+Due to the applet security constraints, PDB Files can currently only be
+imported by cut and paste of the PDB file text into the text box opened
+by the 'From File' entry of the structure menu.</em></p>
+
<p><strong>Viewing the PDB Residue Numbering</strong><br>
Sequences which have PDB entry or PDB file associations are annotated
with sequence features from a group named with the associated PDB
-accession number or file name. Each feature gives the corresponding
-PDB Residue Number for each mapped residue in the seuqence. The
-display of these features is controlled through the
-<strong>"View→Sequence Features"</strong> menu item
-and the <a href="featuresettings.html">Feature Settings dialog
-box</a>.</p>
+accession number or file name. Each feature gives the corresponding PDB
+Residue Number for each mapped residue in the sequence. The display of
+these features is controlled through the <strong>"View→Sequence
+Features"</strong> menu item and the <a href="featuresettings.html">Feature
+Settings dialog box</a>.</p>
+
+<p><em><strong>Outstanding problem with cut'n'pasted
+files in Jalview 2.6 and Jalview 2.7</strong><br>
+Structures imported via the cut'n'paste dialog box will not be correctly
+highlighted or coloured when they are displayed in structure views,
+especially if they contain more than one PDB structure. See the bug
+report at http://issues.jalview.org/browse/JAL-623 for news on this problem.</em></p>
</body>
</html>
+