3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ 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
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>The Chimera PDB Viewer</title>
27 <strong>The Chimera Viewer</strong>
30 Since Jalview 2.8.2, <a href="http://www.cgl.ucsf.edu/chimera/">Chimera</a>
31 (http://www.cgl.ucsf.edu/chimera/) can be used for viewing
32 structures opened via the <a href="structurechooser.html"><strong>"View
33 Structure Data.."</strong> dialog</a>.
36 You can set a default choice of Jmol or Chimera structure viewer in
37 <a href="preferences.html#structure"> Preferences</a>. You can also
38 optionally specify the path to the Chimera program here (if it
39 differs from the standard paths searched by Jalview).<br /> <strong>Please
40 make sure your version of Chimera is up to date. Jalview requires
41 at least Chimera version 1.11.1</strong>
44 If you save your Jalview session as a project file, the state of any
45 open Chimera windows will also be saved, and can be reopened by
46 loading the project file on any machine with Chimera installed. <em>Since
49 <a name="align"><strong>Superposing structures based on
50 their aligned sequences</strong></a><br> If several structures are
51 available on the alignment, you may add additional structures to an
52 existing Chimera view by selecting their entry in the appropriate
53 pop-up menu. Jalview will ask you if you wish to add the structure
54 to the existing alignment, and if you do, it will import and
55 superimpose the new PDB file using the corresponding positions from
56 the alignment. If the alignment is subsequently edited, you can use
57 the <a href="#sAlign"><em>Chimera→Align</em></a> menu option
58 from the menu bar of the structure view window to superpose the
59 structures using the updated alignment.<br>
62 <strong>Chimera Controls</strong><br> The structure is by
63 default rendered as a ribbon diagram. Moving the mouse over the
64 structure brings up tooltips giving the residue name, PDB residue
65 number and chain code ([RES]Num:Chain). Moving the mouse over an
66 associated residue in an alignment window highlights the associated
67 atoms in the displayed structures. When residues are selected in the
68 Chimera window, they are highlighted on the alignment.
69 <p>For comprehensive details of Chimera's commands, refer to the
72 <strong>Selecting residues in Jalview from Chimera</strong><br />
73 When a selection is highlighted in a Jalview window, use the
74 <em>Select→Select Highlighted Region</em> or press <em>B</em>
75 to add the mapped positions to the alignment window's column
79 Basic screen operations (see <a
80 href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html">Chimera
82 http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html
86 <td><strong>Action</strong></td>
87 <td><strong>Windows</strong></td>
88 <td><strong>Unix</strong></td>
89 <td><strong>Mac/OSX</strong></td>
93 <td>Left Click and Drag</td>
94 <td>Left Click and Drag</td>
95 <td>Left Click and Drag</td>
99 <td>Right Click<br> drag mouse up or down
101 <td>Right Click<br>drag mouse up or down
103 <td>cmd or Right + Click and drag mouse up or down, <br>or
104 use mouse scroll button
109 <td>Middle Button + Drag</td>
110 <td>Middle Button and drag</td>
111 <td>alt + Click<br> and drag
115 <td>Select Residues</td>
116 <td>Ctrl + Click (and drag to select a region)</td>
117 <td>Ctrl + Click (and drag)</td>
118 <td>Ctrl + Click (and drag)</td>
123 <strong>Jalview Controls</strong>
124 <p>The Jalview Chimera View window has up to five menus:</p>
129 <li><strong>View Mapping<br>
130 </strong><em> Opens a text window showing the alignment between the
131 residues corresponding to alpha-carbon atoms in the PDB
132 structure and the residues in the associated sequence.</em></li>
134 <li><strong>View</strong>
136 <li><strong>Show Chains<br>
137 </strong><em>Select which of the PDB file's chains (if more than
138 one) are to be displayed.</em></li>
139 <li><strong>Colour by ..<br></strong><em>Submenu
140 allowing specific alignment views to be selected for
141 colouring associated chains in the structure display. This
142 menu contains all the alignment views associated with the
143 structure view, with those used to colour the view indicated
144 by ticks. Addditionally, it contains the following menu
147 <li><strong>Select many views<br></strong><em>When
148 this option is enabled, selecting an alignment view adds
149 it to the set used to colour the structures. Use this
150 when colouring structures related to a number of
151 alignments involving different domains or chains which
152 are shown in the same structure view.</em></li>
153 <li><strong>Select all views<br></strong><em>This
154 is only enabled when </em><strong>Select many views</strong><em>
155 is also enabled, and will add all associated views to
156 the set used to colour the structure display.</em></li>
157 <li><strong>Invert selection<br></strong><em>This
158 is only enabled when </em><strong>Select many views</strong><em>
159 is also enabled, and will replace the current set of
160 views with any remaining views not currently used to
161 colour the structure display.</em></li>
164 <li><strong>Colours<br>
167 <li><strong>By Sequence<br>
168 </strong><em> Colours each residue in the structure with the colour
169 of its corresponding residue in the associated sequence as
170 rendered in the associated alignment views, including any
171 UniProt sequence features or region colourings.<br />Pick
172 which of the associated alignment views are used to colour
173 the structures using the <strong>View→Colour
174 by ..</strong> sub menu.
175 </em><br> Residues which only exist in the PDB structure are
176 coloured white if they are insertions (relative to the
177 associated sequence in the alignment) and grey if they are N
178 or C terminal flanks outside the region mapped to the
179 alignment window's sequence.</em></li>
180 <li><strong>By Chain<br>
181 </strong><em>Uses the Chimera 'rainbow chain' command to apply a
182 different colour to each chain.</em></li>
183 <li><strong>Charge & Cysteine<br>
184 </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid
185 or Glutamic Acid) residues in red, and cationic (Lysine or
186 Arginine) residues in blue.</em></li>
187 <li><strong>Colour with Chimera<br></strong><em>Defers
188 any colouring operations to Chimera. Select this if you want
189 to use the Chimera scripting interface or menu to modify the
190 view directly.</em></li>
191 <li><strong>Standard and User Defined Jalview
193 </strong><em>The remaining entries apply the colourschemes available
194 from the standard and user defined <a
195 href="../colourSchemes/index.html">amino acid
199 <li><strong>Chimera<br>
200 </strong><em>This pulldown menu is only displayed if there are multiple
201 structures shown in the Chimera window, and Jalview can also
202 locate at least two of the structures in the currently
203 associated alignment view.</em>
205 <li><strong><a name="sAlign">Align</a> <br> </strong><em>
206 When selected, the associated alignment will be used to
207 superimpose all the structures in the view onto the first
208 structure in the alignment. The regions used to calculate
209 the superposition will be highlighted using the 'Cartoon'
210 rendering style, and the remaining data shown as a chain
217 <li><strong>Chimera Help<br>
218 </strong><em>Access the Chimera Help documentation in a new browser
223 <strong>Chimera and Windows Firewall</strong>
225 Jalview and Chimera communicate using Chimera's
227 href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html">REST
229 (http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html).
230 <br> Technically this requires both Chimera and Jalview to open
231 ports on the local network, and this may be blocked by Windows
232 Firewall with a warning message such as
233 <br /> "Windows Firewall has blocked some features of this program"
234 (where the program may be jp2launcher.exe for Jalview Webstart, or
235 java.exe or javaw.exe for the InstallAnywhere version).
236 <br /> To allow Jalview and Chimera to interact, you may need to add
237 permission for the program to communicate over the network. This can
238 be done from the warning dialogue, or in Control Panel, Firewall