-<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 \r
- can visualize polypeptide backbone structures associated with a sequence in \r
- a particular alignment view. It is accessed via the <strong>"Strucutre→View \r
- PDB entry:"</strong> entry from the sequence's <a\r
- href="../menus/popupMenu.html">pop-up menu</a>.</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
- "Structure<strong>→</strong> Associate Structure with Sequence", \r
- 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
- 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
-<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
+<html>
+<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>
git://source.jalview.org / jalview.git / blobdiff