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