+#-------------------------------------------------------------------------------
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
+# Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+#
+# This file is part of Jalview.
+#
+# Jalview is free software: you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+#
+# Jalview is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty
+# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+# 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/>.
+#-------------------------------------------------------------------------------
<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * 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 has a simple <a href="pdbviewer.html">3D structure viewer</a> which can visualize polypeptide backbone
- structures associated with a sequence in a particular alignment view. It is
- accessed via the <strong>"Sequence→View PDB
- entry:"</strong> entry from the sequence's <a
- href="../menus/popupMenu.html">pop-up menu</a>.</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
- "Associate Structure with Sequence", and one of the submenus:</p>
+ "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
- can be saved in the Jalview Archive file. <br>
+ 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>
PDB ids for all the sequences in the alignment which have valid Uniprot names
/ accession ids. </li>
</ul>
-<p><strong>Note:</strong> You can retrieve sequences from the PDB using the <a
+<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).</p>
-<p>See the <a
-href="pdbviewer.html">PDB Viewer</a> help page for more information. </p> </p>
+ 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