3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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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. For
69 comprehensive details of Chimera's commands, refer to the tool's
72 Basic screen operations (see <a
73 href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html">Chimera
75 http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html
79 <td><strong>Action</strong></td>
80 <td><strong>Windows</strong></td>
81 <td><strong>Unix</strong></td>
82 <td><strong>Mac/OSX</strong></td>
86 <td>Left Click and Drag</td>
87 <td>Left Click and Drag</td>
88 <td>Left Click and Drag</td>
92 <td>Right Click<br> drag mouse up or down
94 <td>Right Click<br>drag mouse up or down
96 <td>cmd or Right + Click and drag mouse up or down, <br>or
97 use mouse scroll button
102 <td>Middle Button + Drag</td>
103 <td>Middle Button and drag</td>
104 <td>alt + Click<br> and drag
108 <td>Select Residues</td>
109 <td>Ctrl + Click (and drag to select a region)</td>
110 <td>Ctrl + Click (and drag)</td>
111 <td>Ctrl + Click (and drag)</td>
116 <strong>Jalview Controls</strong>
117 <p>The Jalview Chimera View window has up to five menus:</p>
122 <li><strong>View Mapping<br>
123 </strong><em> Opens a text window showing the alignment between the
124 residues corresponding to alpha-carbon atoms in the PDB
125 structure and the residues in the associated sequence.</em></li>
127 <li><strong>View</strong>
129 <li><strong>Show Chains<br>
130 </strong><em>Select which of the PDB file's chains (if more than
131 one) are to be displayed.</em></li>
132 <li><strong>Colour by ..<br></strong><em>Submenu
133 allowing specific alignment views to be selected for
134 colouring associated chains in the structure display. This
135 menu contains all the alignment views associated with the
136 structure view, with those used to colour the view indicated
137 by ticks. Addditionally, it contains the following menu
140 <li><strong>Select many views<br></strong><em>When
141 this option is enabled, selecting an alignment view adds
142 it to the set used to colour the structures. Use this
143 when colouring structures related to a number of
144 alignments involving different domains or chains which
145 are shown in the same structure view.</em></li>
146 <li><strong>Select all views<br></strong><em>This
147 is only enabled when </em><strong>Select many views</strong><em>
148 is also enabled, and will add all associated views to
149 the set used to colour the structure display.</em></li>
150 <li><strong>Invert selection<br></strong><em>This
151 is only enabled when </em><strong>Select many views</strong><em>
152 is also enabled, and will replace the current set of
153 views with any remaining views not currently used to
154 colour the structure display.</em></li>
157 <li><strong>Colours<br>
160 <li><strong>By Sequence<br>
161 </strong><em> Colours each residue in the structure with the colour
162 of its corresponding residue in the associated sequence as
163 rendered in the associated alignment views, including any
164 UniProt sequence features or region colourings.<br />Pick
165 which of the associated alignment views are used to colour
166 the structures using the <strong>View→Colour
167 by ..</strong> sub menu.
168 </em><br> Residues which only exist in the PDB structure are
169 coloured white if they are insertions (relative to the
170 associated sequence in the alignment) and grey if they are N
171 or C terminal flanks outside the region mapped to the
172 alignment window's sequence.</em></li>
173 <li><strong>By Chain<br>
174 </strong><em>Uses the Chimera 'rainbow chain' command to apply a
175 different colour to each chain.</em></li>
176 <li><strong>Charge & Cysteine<br>
177 </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid
178 or Glutamic Acid) residues in red, and cationic (Lysine or
179 Arginine) residues in blue.</em></li>
180 <li><strong>Colour with Chimera<br></strong><em>Defers
181 any colouring operations to Chimera. Select this if you want
182 to use the Chimera scripting interface or menu to modify the
183 view directly.</em></li>
184 <li><strong>Standard and User Defined Jalview
186 </strong><em>The remaining entries apply the colourschemes available
187 from the standard and user defined <a
188 href="../colourSchemes/index.html">amino acid
192 <li><strong>Chimera<br>
193 </strong><em>This pulldown menu is only displayed if there are multiple
194 structures shown in the Chimera window, and Jalview can also
195 locate at least two of the structures in the currently
196 associated alignment view.</em>
198 <li><strong><a name="sAlign">Align</a> <br> </strong><em>
199 When selected, the associated alignment will be used to
200 superimpose all the structures in the view onto the first
201 structure in the alignment. The regions used to calculate
202 the superposition will be highlighted using the 'Cartoon'
203 rendering style, and the remaining data shown as a chain
210 <li><strong>Chimera Help<br>
211 </strong><em>Access the Chimera Help documentation in a new browser
216 <strong>Chimera and Windows Firewall</strong>
218 Jalview and Chimera communicate using Chimera's
220 href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html">REST
222 (http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html).
223 <br> Technically this requires both Chimera and Jalview to open
224 ports on the local network, and this may be blocked by Windows
225 Firewall with a warning message such as
226 <br /> "Windows Firewall has blocked some features of this program"
227 (where the program may be jp2launcher.exe for Jalview Webstart, or
228 java.exe or javaw.exe for the InstallAnywhere version).
229 <br /> To allow Jalview and Chimera to interact, you may need to add
230 permission for the program to communicate over the network. This can
231 be done from the warning dialogue, or in Control Panel, Firewall