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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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.
- *
+ * 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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+ * 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 Viewer</title>
+</head>
+<body>
+<p><strong>The Jalview internal PDB Viewer</strong><br>
+Since Jalview 2.3, the <a href="jmol.html">Jmol PDB Viewer</a> is
+the main method for <a href="viewingpdbs.html">viewing PDB
+structures</a>. The documentation below concerns the original Jalview
+PDB viewer, which is only used in situations where Jmol is unavailable
+or cannot operate.</p>
+<p><strong>The PDB Viewer Window</strong>
+<p>This interactive structure viewing window is opened by selecting
+entries from the <strong>"Structure→"</strong> submenu
+ of the <a href="../menus/popupMenu.html">sequence
+ id pop-up menu</a>. The internal PDB viewer is not able to show
+ superpositions, so no other options are provided. Structures can only
+ be viewed for sequences which have an <a href="viewingpdbs.html">associated
+PDB structure</a>, and the PDB Viewer will only be associated with the
+particular alignment view from which it was opened.</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>
+ <!-- NOT YET IMPLEMENTED <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>
git://source.jalview.org / jalview.git / blobdiff