-<html>\r
-<head><title>PDB Viewing</title></head>\r
-<body>\r
-<p><strong>Viewing PDB Structures</strong></p>\r
-<p>Jalview has a simple <a href="pdbviewer.html">3D structure viewer</a> which can visualize polypeptide backbone\r
- structures associated with a sequence in an alignment. It is\r
- accessed via the <strong>"Sequence→View PDB\r
- entry:"</strong> entry from the sequence's <a\r
- href="../menus/popupMenu.html">pop-up menu</a>.</p>\r
-<p>To associate PDB files with a sequence, right click on a sequence ID and select \r
- "Associate Structure with Sequence", and one of the submenus:</p>\r
-<ul>\r
- <li>From File - You can load a PDB file from the local machine or network and \r
- associate it with the selected sequence. PDB files associated in this way \r
- can be saved in the Jalview Archive file. <br>\r
- </li>\r
- <li>Enter PDB Id - Jalview will use WSDBFetch, provided by the EBI, to fetch \r
- the PDB file with the entered Id.<br>\r
- </li>\r
- <li>Discover PDB Ids - Jalview uses WSDBFetch, provided by the EBI, to discover \r
- PDB ids for all the sequences in the alignment which have valid Uniprot names \r
- / accession ids. </li>\r
-</ul>\r
-<p><strong>Note:</strong> You can retrieve sequences from the PDB using the <a\r
- href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with this \r
- service are automatically associated with their source database entry. For PDB \r
- sequences, simply select PDB as the database and enter your known PDB id (appended \r
- with ':' and a chain code, if desired).</p>\r
-<p>For help on viewing and colouring structures see the <a\r
-href="pdbviewer.html">PDB Viewer</a> help page. </p> </p>\r
-</body>\r
-</html>\r
+<html>
+<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>
+<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>
+</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>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff