-<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>