<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>PDB Viewing</title>
<li>If the structure is already shown, then you will be prompted
to associate the sequence with an existing view of the selected
- structure.</li>
+ structure. This is useful when working with multi-domain or multi-chain PDB files.</li>
<li style="list-style: none">See the <a href="jmol.html">Jmol
PDB viewer</a> help page for more information about the display.</li>
</ul>
-
-
-<p>To associate PDB files with a sequence, right click on a sequence
+ <p>
+ <em>Opening structures associated with the current selection</em><br />
+ If one or more of the sequences in the alignment are selected, then
+ the Structure submenu of the <a href="../menus/popupMenu.html">Sequence
+ ID popup menu</a> will contain will include either a 'View all <em>X</em>
+ structures' entry in the submenu or a 'View structure for <em>Sequence</em>'
+ entry. Both these options will open a new Jmol view containing one, or
+ all the structures available for all selected sequences, superimposed
+ using the currently selected region of the alignment. (<em>This
+ capability was added in Jalview 2.7</em>)
+ </p>
+ <p><strong>Associating PDB files with Sequences</strong></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>
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>
+ <li>Discover PDB Ids - Jalview uses the sequence's ID to query WSDBFetch, provided by the
+ EBI, and any enabled DAS servers, to discover PDB ids associated with the sequence.</li>
</ul>
<p><strong>Importing PDB Entries or files in PDB format</strong><br>
git://source.jalview.org / jalview.git / blobdiff