3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
4 * Copyright (C) 2014 The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 <title>PDB Viewer</title>
24 <p><strong>The Jalview internal PDB Viewer</strong><br>
25 Since Jalview 2.3, the <a href="jmol.html">Jmol PDB Viewer</a> is
26 the main method for <a href="viewingpdbs.html">viewing PDB
27 structures</a>. The documentation below concerns the original Jalview
28 PDB viewer, which is only used in situations where Jmol is unavailable
29 or cannot operate.</p>
30 <p><strong>The PDB Viewer Window</strong>
31 <p>This interactive structure viewing window is opened by selecting
32 entries from the <strong>"Structure→"</strong> submenu
33 of the <a href="../menus/popupMenu.html">sequence
34 id pop-up menu</a>. The internal PDB viewer is not able to show
35 superpositions, so no other options are provided. Structures can only
36 be viewed for sequences which have an <a href="viewingpdbs.html">associated
37 PDB structure</a>, and the PDB Viewer will only be associated with the
38 particular alignment view from which it was opened.</p>
39 <p><strong>Controls</strong></p>
40 <p>The structure is rendered as an alpha-carbon trace. Moving the
41 mouse over the structure brings up tooltips with a residue name and PDB
42 sequence position. If a mapping exists to a residue in the associated
43 sequence, then this will be highlighted in the associated view in its
44 alignment window, and vice versa for viewing the coordinates associated
45 with a particular residue in the sequence in a particular view on the
47 <p>Selecting a residue highlights its associated sequence residue
48 and alpha carbon location.</p>
52 <td><strong>Action</strong></td>
53 <td><strong>Windows</strong></td>
54 <td><strong>Unix</strong></td>
55 <td><strong>Mac/OSX</strong></td>
67 <td>Left Click and Drag</td>
68 <td>Left Click and Drag</td>
69 <td>Click and Drag</td>
73 <td>Right Click and drag</td>
74 <td>Right Click and Drag</td>
79 <td>Middle-Button and Drag</td>
80 <td>Middle-Button and Drag</td>
97 <p>There are three menus:
102 <li><strong>Save As<br>
103 </strong><em>Saves the current view as an EPS or PNG file.</em></li>
104 <li><strong>View Mapping<br>
105 </strong><em> Opens a text window showing the alignment between the
106 residues corresponding to alpha-carbon atoms in the PDB structure and
107 the residues in the associated sequence.</em></li>
110 <li><strong>Colours<br>
113 <li><strong>By Sequence<br>
114 </strong><em> Colours each residue in the structure with the colour of its
115 corresponding residue in the associated sequence as rendered in the
116 associated alignment view, including any Uniprot sequence features or
117 region colourings.<br>
118 Residues which only exist in the PDB structure are coloured white if
119 they are insertions (relative to the associated sequence in the
120 alignment) and grey if they are N or C terminal flanks outside the
121 region mapped to the alignment window's sequence.</em></li>
122 <li><strong>By Chain<br>
123 </strong><em> Assigns a random colour to each PDB chain.</em>
124 <li><strong>Charge & Cysteine<br>
125 </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
126 Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
127 residues in blue.</em></li>
128 <li><strong><em>Standard and User Defined Jalview
130 </em></strong> The remaining entries apply the colourschemes available from the
131 standard and user defined <a href="../colourSchemes/index.html">amino
132 acid colours</a>.</em></li>
136 </strong><em> These options can be turned off to improve performance when
137 viewing large structures, some at the expense of visual clarity.</em>
139 <li><strong>Wireframe<br>
140 </strong><em> Draws thin lines rather than thick lines for the
141 alpha-carbon trace.</em></li>
142 <li><strong>Depthcue<br>
143 </strong><em>Shades the structure so parts of the structure near the front
144 of the view are brighter than those further away.</em></li>
145 <li><strong>Z Buffering<br>
146 </strong><em> Applies depth sorting to correctly render occluded regions
147 of the backbone trace.</em></li>
148 <li><strong>Show All Chains<br>
149 </strong><em> When turned on, shows all chains in the PDB file, not just
150 the one associated with a sequence in the alignment window.</em></li>
151 <!-- NOT YET IMPLEMENTED <li><strong>Associate View</strong><br>
152 Change which view on the associated sequence's alignment is to be
153 associated with the PDB viewer.-->
158 <p><strong>Notes for PDB Viewing in the Jalview Applet</strong>
159 <p>The applet can only load PDB files by copying and pasting the
160 text into the popup window which appears when "Show PDB
161 Structure" is selected after right clicking on a sequence name.</p>