<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
+<p>Jalview has a simple <a href="pdbviewer.html">3D structure viewer</a> which \r
+ can visualize polypeptide backbone structures associated with a sequence in \r
+ a particular alignment view. It is accessed via the <strong>"Sequence→View \r
+ PDB entry:"</strong> entry from the sequence's <a\r
href="../menus/popupMenu.html">pop-up menu</a>.</p>\r
-<p>There are two ways to associate PDB files with sequences:</p>\r
+<p>Since Jalview 2.3, Jmol has been integrated into the application and will also \r
+ run in the applet in all latest web browsers. For more help using Jmol, see \r
+ <a href="http://jmol.sourceforge.net/docs/JmolUserGuide/">http://jmol.sourceforge.net/docs/JmolUserGuide/</a> \r
+</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>Select "<a href="seqfeatures.html">Sequence Features</a>" from\r
- the "View" menu, which retrieves any uniprot sequence\r
- records associated with the sequences in the alignment. If, for a\r
- particular sequence's uniprot record there\r
- are any cross-references to PDB structures, then these will be\r
- added to its list of associated database ids.</li>\r
- <li>Retrieve sequences from the PDB using the <a\r
- href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved\r
- with this service are automatically associated with their source\r
- database entry. For PDB sequences, simply select PDB as the database\r
- and enter your known PDB id (appended with ':' and a chain code, if\r
- desired).</li>\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
+ will also be saved in the <a href="jalarchive.html">Jalview Archive file</a>. <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
-For help on viewing and colouring structures see the <a\r
-href="pdbviewer.html">PDB Viewer</a> help page.\r
-</p>\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>Sequences which have PDB File associations are annotated with sequence features \r
+ from the group 'PDBFile' giving the corresponding PDB Residue Number for each \r
+ mapped residue in the seuqence. The display of these features is controlled through\r
+ the <strong>"View→Sequence Features"</strong> menu item and the \r
+ <a href="featuresettings.html">Feature Settings dialog box</a>.</p> \r
+<p>See the <a\r
+href="pdbviewer.html">PDB Viewer</a> help page for more information. </p> </p>\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / blobdiff