-<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>
+ <br/>
+ <hr>
+ <p>
+ <strong>Switching between mmCIF and PDB format for
+ downloading files from the PDB</strong><br /> Jalview now employs the <a
+ href="mmcif.html">mmCIF format</a> for importing 3D structure data
+ from flat file and EMBL-PDBe web-service, as recommended by the
+ wwwPDB. If you prefer (for any reason) to download data as PDB files
+ instead, then first close Jalview, and add the following line to
+ your .jalview_properties file:<br />
+ <code> PDB_DOWNLOAD_FORMAT=PDB </code>
+ <br /> When this setting is configured, Jalview will only request
+ PDB format files from EMBL-EBI's PDBe.<br /> <em>mmCIF format
+ file support was added in Jalview 2.10.</em>
+ </p>