<html>
-<head>
-<title>PDB Viewer</title>
-</head>
-<body>
-<p><strong>The PDB Viewer Window</strong>
-<p>This interactive structure viewing window is opened by selecting
-the <strong>"Sequence→View PDB entry:"</strong> entry in
-the <a href="../menus/popupMenu.html">sequence id pop-up menu</a>. This
-can only be done for sequences which have an <a href="viewingpdbs.html">associated
-PDB structure</a>.</p>
-<p><strong>Controls</strong></p>
-<p>The structure is rendered as an alpha-carbon trace. Moving the
-mouse over the structure brings up tooltips with a residue name and PDB
-sequence position. If a mapping exists to a residue in the associated
-sequence, then this will be highlighted in the associated view in its
-alignment window, and vice versa for viewing the coordinates associated
-with a particular residue in the sequence in a particular view on the
-alignment.</p>
-<p>Selecting a residue highlights its associated sequence residue
-and alpha carbon location.</p>
-<p>
-<table>
- <tr>
- <td><strong>Action</strong></td>
- <td><strong>Windows</strong></td>
- <td><strong>Unix</strong></td>
- <td><strong>Mac/OSX</strong></td>
- </tr>
- <tr>
- <td>Select/<br>
- Deselect<br>
- Residue</td>
- <td>Left Click</td>
- <td>Left Click</td>
- <td>Click</td>
- </tr>
- <tr>
- <td>Rotate View</td>
- <td>Left Click and Drag</td>
- <td>Left Click and Drag</td>
- <td>Click and Drag</td>
- </tr>
- <tr>
- <td>Roll View</td>
- <td>Right Click and drag</td>
- <td>Right Click and Drag</td>
- <td>TODO</td>
- </tr>
- <tr>
- <td>Move Origin</td>
- <td>Middle-Button and Drag</td>
- <td>Middle-Button and Drag</td>
- <td>TODO</td>
- </tr>
- <tr>
- <td>Zoom In</td>
- <td>Up Arrow</td>
- <td>Up Arrow</td>
- <td>Up Arrow</td>
- </tr>
- <tr>
- <td>Zoom Out</td>
- <td>Down Arrow</td>
- <td>Down Arrow</td>
- <td>Down Arrow</td>
- </tr>
-</table>
-</p>
-<p>There are three menus:
-<ul>
- <li><Strong>File<br>
- </strong>
- <ul>
- <li><strong>Save As<br>
- </strong><em>Saves the current view as an EPS or PNG file.</em></li>
- <li><strong>View Mapping<br>
- </strong><em> Opens a text window showing the alignment between the
- residues corresponding to alpha-carbon atoms in the PDB structure and
- the residues in the associated sequence.</em></li>
- </ul>
- </li>
- <li><strong>Colours<br>
- </strong>
- <ul>
- <li><strong>By Sequence<br>
- </strong><em> Colours each residue in the structure with the colour of its
- corresponding residue in the associated sequence as rendered in the
- associated alignment view, including any Uniprot sequence features or
- region colourings.<br>
- Residues which only exist in the PDB structure are coloured white if
- they are insertions (relative to the associated sequence in the
- alignment) and grey if they are N or C terminal flanks outside the
- region mapped to the alignment window's sequence.</em></li>
- <li><strong>By Chain<br>
- </strong><em> Assigns a random colour to each PDB chain.</em>
- <li><strong>Charge & Cysteine<br>
- </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
- Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
- residues in blue.</em></li>
- <li><strong><em>Standard and User Defined Jalview
- colourschemes.<br>
- </em></strong> The remaining entries apply the colourschemes available from the
- standard and user defined <a href="../colourSchemes/index.html">amino
- acid colours</a>.</em></li>
- </ul>
- </li>
- <li><strong>View<br>
- </strong><em> These options can be turned off to improve performance when
- viewing large structures, some at the expense of visual clarity.</em>
- <ul>
- <li><strong>Wireframe<br>
- </strong><em> Draws thin lines rather than thick lines for the
- alpha-carbon trace.</em></li>
- <li><strong>Depthcue<br>
- </strong><em>Shades the structure so parts of the structure near the front
- of the view are brighter than those further away.</em></li>
- <li><strong>Z Buffering<br>
- </strong><em> Applies depth sorting to correctly render occluded regions
- of the backbone trace.</em></li>
- <li><strong>Show All Chains<br>
- </strong><em> When turned on, shows all chains in the PDB file, not just
- the one associated with a sequence in the alignment window.</em></li>
- <li><strong>Associate View</strong><br>
- Change which view on the associated sequence's alignment is to be
- associated with the PDB viewer.
- </ul>
- </li>
-</ul>
-</p>
-<p><strong>Notes for PDB Viewing in the Jalview Applet</strong>
-<p>The applet can only load PDB files by copying and pasting the
-text into the popup window which appears when "Show PDB
-Structure" is selected after right clicking on a sequence name.</p>
-</body>
-</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/>.
+-->
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