-<html>\r
-<head><title>PDB Viewer</title></head>\r
-<body>\r
-<p><strong>Viewing PDB Structures</strong></p>\r
-<p>Jalview has a simple 3D structure viewer which can load PDB files and associate \r
- the structure with a sequence in an alignment. </p>\r
-<p>There are 2 ways to load and associate a PDB file into Jalview application.</p>\r
-<ul>\r
- <li>Select "<a href="seqfeatures.html">Sequence Features</a>" from \r
- the "View" menu. This will attempt to match your sequences with \r
- the Uniprot database first by name, then by sequence. The same process will \r
- make note of any PDB files associated with each sequence. </li>\r
- <li>Select "<a href="seqfetch.html">Fetch Sequence</a>" from an alignment \r
- window or from the main desktop "File" menu. In the popup window \r
- which appears, select PDB as the database and enter your known PDB id. If \r
- you know which chain you wish to retrieve, append the chain id after a colon \r
- eg 1GAQ:B</li>\r
-</ul>\r
-<p>Note the applet can only load PDB files by copying and pasting the text into \r
- the popup window which appears when "Show PDB Structure" is selected \r
- after right clicking on a sequence name.</p>\r
-<p>To see a particular structure, right click on a sequence name and from the \r
- popup menu select "Sequence -> View PDB Entry". </p>\r
-<p>The PDB Structure viewer will perform a pairwise alignment of your sequence \r
- and each PDB chain sequence. To view the results of the mapping, select "File \r
- -> View Mapping" from the structure viewer window. </p>\r
-<p>Moving the mouse over the structure will highlight the residue in the alignment \r
- window, and vice versa.</p>\r
-<p>"Colour by Charge/Cysteine" will colour all Aspartate and Glutamate \r
- residues red, Lysine and Arginine will be blue and Cysteine residues will be \r
- coloured yellow.</p>\r
-<p><em>Tips for Viewing Structures</em></p>\r
-<ul>\r
- <li>Colour By Sequence follows the exact colours of the alignment window, including \r
- sequence features. Thus you can easily view Uniprot sequence features, eg \r
- helix or metal binding sites on both the alignment and structure viewer.</li>\r
- <li>Deselect Colours->Show All Chains in order to view only the mapped chain. \r
- </li>\r
- <li>Use Wireframe, without depthcue, and without Z Buffering in order to accelerate \r
- the rendering of the structure. </li>\r
- <li>You can save an image of your structure as a PNG or EPS file.</li>\r
- <li>Use the cursor keys Up and Down arrow to zoom in and zoom out</li>\r
-</ul>\r
-</body>\r
-</html>\r
+<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/>.
+-->
git://source.jalview.org / jalview.git / blobdiff