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+<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/popUp.html">pop-up menu</a>.</p>\r
+<p>There are two ways to associate PDB files with sequences:</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
+</ul>\r
+For help on viewing and colouring structures see the <a\r
+href="pdbviewer.html">PDB Viewer</a> help page. \r
+</p>\r
+</body>\r
+</html>\r
git://source.jalview.org / jalview.git / commitdiff