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- * 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 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
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+ * of the License, or (at your option) any later version.
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* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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+ * 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.
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<head>
<title>PDB Viewing</title>
</head>
<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>. Once a pdb
+via the <strong>"Structure→"</strong> submenu from a
+sequence's <a href="../menus/popupMenu.html">pop-up menu</a>.</p>
+<p>The following menu entries are provided for viewing structure data<br>
+ <ul>
+ <li>The <strong>"Structure→View
+ Structure→</strong> submenu allows a single PDB structure to be chosen
+ for display from the available structures for a sequence.
+ </li>
+ <li>The <strong>"Structure→View all <em>N</em>
+ structures
+ </strong> option will open a new window containing all structures associated
+ with the current selection, superposed according to the currently selected region of the alignment.<br/><em>This
+ capability was added in Jalview 2.7</em>
+ </li>
+ <li><a name="viewreps"/>The <strong>"Structure→View all <em>N</em>
+ representative structures
+ </strong> option will open a new window containing exactly one structure per
+ currently selected sequence.<br />
+ <em>The View representative structures option was introduced in
+ Jalview 2.8.1</em></li>
+ </ul>
+ <br>
+</p>
+
+<p>If a single pdb
structure is selected, one of the following will happen:</p>
<ul>
<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><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