<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 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>, 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>
+ <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>
+ </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