* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
---!>
-<head><title>PDB Viewing</title></head>
-<body>
-<p><strong>Viewing PDB Structures</strong></p>
-<p>Jalview can view protein structures associated with a sequence via the <strong>"Structure→View
- PDB entry:"</strong> entries from a sequence's <a
- href="../menus/popupMenu.html">pop-up menu</a>. This will open an
- interactive display of the structure in a new window, or prompt you
- to associate the sequence with an existing view of the selected
- structure. See the <a href="jmol.html">Jmol PDB viewer</a> help page
- for more information about the display.
-</p>
-<p>To associate PDB files with a sequence, right click on a sequence ID and select
- "Structure<strong>→</strong> 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>Importing PDB Entries or files in PDB format</strong><br>
-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).
-<br>Jalview will also read PDB files directly. Simply load in the file
-as you would an alignment file. The sequences of any peptide chains
-will be extracted from the file and viewed in the alignment window.
-<br><em>Note for jalview applet users: 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.</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 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>
-</body>
-</html>
+-->