2 <head><title>PDB Viewing</title></head>
4 <p><strong>Viewing PDB Structures</strong></p>
5 <p>Jalview has a simple <a href="pdbviewer.html">3D structure viewer</a> which can visualize polypeptide backbone
6 structures associated with a sequence in a particular alignment view. It is
7 accessed via the <strong>"Sequence→View PDB
8 entry:"</strong> entry from the sequence's <a
9 href="../menus/popupMenu.html">pop-up menu</a>.</p>
10 <p>To associate PDB files with a sequence, right click on a sequence ID and select
11 "Associate Structure with Sequence", and one of the submenus:</p>
13 <li>From File - You can load a PDB file from the local machine or network and
14 associate it with the selected sequence. PDB files associated in this way
15 will also be saved in the <a href="jalarchive.html">Jalview Archive file</a>. <br>
17 <li>Enter PDB Id - Jalview will use WSDBFetch, provided by the EBI, to fetch
18 the PDB file with the entered Id.<br>
20 <li>Discover PDB Ids - Jalview uses WSDBFetch, provided by the EBI, to discover
21 PDB ids for all the sequences in the alignment which have valid Uniprot names
22 / accession ids. </li>
24 <p><strong>Note:</strong> You can retrieve sequences from the PDB using the <a
25 href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with this
26 service are automatically associated with their source database entry. For PDB
27 sequences, simply select PDB as the database and enter your known PDB id (appended
28 with ':' and a chain code, if desired).</p>
29 <p>Sequences which have PDB File associations are annotated with sequence features
30 from the group 'PDBFile' giving the corresponding PDB Residue Number for each
31 mapped residue in the seuqence. The display of these features is controlled through
32 the <strong>"View→Sequence Features"</strong> menu item and the
33 <a href="featuresettings.html">Feature Settings dialog box</a>.</p>
35 href="pdbviewer.html">PDB Viewer</a> help page for more information. </p> </p>