+#-------------------------------------------------------------------------------
+# 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
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