<html>
-<head><title>PDB Viewing</title></head>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
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+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
+<head>
+<title>PDB Viewing</title>
+</head>
<body>
<p><strong>Viewing PDB Structures</strong></p>
-<p>Jalview has a simple <a href="pdbviewer.html">3D structure viewer</a> which can visualize polypeptide backbone
- structures associated with a sequence in a particular alignment view. It is
- accessed via the <strong>"Sequence→View PDB
- entry:"</strong> entry from the sequence's <a
- href="../menus/popupMenu.html">pop-up menu</a>.</p>
-<p>To associate PDB files with a sequence, right click on a sequence ID and select
- "Associate Structure with Sequence", and one of the submenus:</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
+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
+ PDB viewer</a> help page for more information about the display.</li>
</ul>
-<p><strong>Note:</strong> 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).</p>
- <p>Sequences which have PDB File associations are annotated with sequence features
- from the group 'PDBFile' giving 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>
-<p>See the <a
-href="pdbviewer.html">PDB Viewer</a> help page for more information. </p> </p>
+ <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
+ 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 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>
+
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