3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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16 * PURPOSE. See the GNU General Public License for more details.
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20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>The Jmol PDB Viewer</title>
26 <p><strong>The Jmol PDB Viewer</strong></p>
27 <p>Since Jalview 2.3, <a href="http://jmol.sourceforge.net/">Jmol</a>
28 has been integrated into Jalview for interactively viewing structures
29 opened by entries in the <strong>"Structure"</strong> submenu in the <a href="../menus/popupMenu.html">sequence
30 id pop-up menu</a> (if you can't see this, then you need to <a
31 href="viewingpdbs.html">associate a PDB structure</a> with the
32 sequence). Jmol is available from the Jalview desktop and should also
33 run in the JalviewLite applet, providing the browser supports Java 1.5.
34 If Jmol is not available, then the original <a href="pdbviewer.html">internal
35 pdb viewer</a> will be used as a fallback.</p>
36 <!-- <p>The following menu entries are provided for viewing structure data<br>
38 <li>The <strong>"Structure→View
39 Structure→</strong> submenu allows a single PDB structure to be chosen
40 for display from the available structures for a sequence.
42 <li>The <strong>"Structure→View all <em>N</em>
44 </strong> option will open a new window containing all structures associated
45 with the current selection.
47 <li>The <strong>"Structure→View all <em>N</em>
48 representative structures
49 </strong> option will open a new window containing exactly one structure per
50 currently selected sequence.<br />
51 <em>The View representative structures option was introduced in
52 Jalview 2.8.1</em></li>
56 <p><a name="align"><strong>Superposing structures based
57 on their aligned sequences</strong></a><br>
58 If several structures are available on the alignment, you may add
59 additional structures to an existing Jmol view by selecting their entry
60 in the appropriate pop-up menu. Jalview will ask you if you wish to add
61 the structure to the existing alignment, and if you do, it will import
62 and superimpose the new PDB file using the corresponding positions from
63 the alignment. If the alignment is subsequently edited, you can use the
64 <a href="#sAlign"><em>Jmol→Align</em></a> menu option from the
65 menu bar of the structure view window to superpose the structures using
66 the updated alignment.<br>
67 <em>Sequence based structure superposition was added in Jalview 2.6</em>
69 <p><strong>Controls</strong><br>
70 The structure is by default rendered as a ribbon diagram. Moving the
71 mouse over the structure brings up tooltips giving the residue name, PDB
72 residue number and chain code, atom name and number
73 ([RES]Num:Chain.AtomName#AtomNumber). If a mapping exists to a residue
74 in any associated sequences, then this will be highlighted in each one's
75 alignment window. The converse also occurs - moving the mouse over an
76 associated residue in an alignment window highlights the associated
77 atoms in the displayed structures.</p>
78 <p>Selecting a residue highlights its associated sequence residue
79 and alpha carbon location. Double clicking an atom allows distances to
80 be measured from it to any other atom in the structure.</p>
84 <td><strong>Action</strong></td>
85 <td><strong>Windows</strong></td>
86 <td><strong>Unix</strong></td>
87 <td><strong>Mac/OSX</strong></td>
91 <td>Left Click and Drag</td>
92 <td>Left Click and Drag</td>
93 <td>Click and Drag</td>
97 <td>Shift + Left Click<br>
98 drag mouse up or down</td>
99 <td>Shift + Left Click<br>
101 drag mouse up or down</td>
102 <td>Left-Alt + Click and drag mouse up or down</td>
114 <td>Shift + Left Click<br>
115 drag mouse to left or right</td>
116 <td>Shift + Left Click<br>
118 drag mouse to left or right</td>
119 <td>Left-Alt + Click and drag mouse to left or right</td>
123 <td>Shift+Control+Left Click<br>
126 <td>Middle-Button<br>
129 <td>Shift+Control+Left Click<br>
141 <p>The window has up to five menus:
146 <li><strong>Save As<br>
147 </strong><em>Save the displayed PDB File, or the current view as an EPS or
149 <li><strong>View Mapping<br>
150 </strong><em> Opens a text window showing the alignment between the
151 residues corresponding to alpha-carbon atoms in the PDB structure and
152 the residues in the associated sequence.</em></li>
155 <li><strong>View</strong>
157 <li><strong>Show Chains<br>
158 </strong><em>Select which of the PDB file's chains are to be displayed.</em></li>
159 <li><strong>Colour by ..<br></strong><em>Submenu allowing specific alignment views to be selected for colouring associated chains in the structure display. This menu contains all the alignment views associated with the structure view, with those used to colour the view indicated by ticks. Addditionally, it contains the following menu entries:</em>
160 <ul><li><strong>Select many views<br></strong><em>When this option is enabled, selecting an alignment view adds it to the set used to colour the structures. Use this when colouring structures related to a number of alignments involving different domains or chains which are shown in the same structure view.</em>
162 <li><strong>Select all views<br></strong><em>This is only enabled when </em><strong>Select many views</strong><em> is also enabled, and will add all associated views to the set used to colour the structure display.</em>
164 <li><strong>Invert selection<br></strong><em>This is only enabled when </em><strong>Select many views</strong><em> is also enabled, and will replace the current set of views with any remaining views not currently used to colour the structure display.</em>
166 <li><strong>Colours<br>
169 <li><strong>By Sequence<br>
170 </strong><em> Colours each residue in the structure with the colour of its
171 corresponding residue in the associated sequence as rendered in the
172 associated alignment views, including any Uniprot sequence features or
173 region colourings.<br/>Pick which of the associated alignment views are used to colour the structures using the <strong>View→Colour by ..</strong> sub menu.</em><br>
174 Residues which only exist in the PDB structure are coloured white if
175 they are insertions (relative to the associated sequence in the
176 alignment) and grey if they are N or C terminal flanks outside the
177 region mapped to the alignment window's sequence.</em></li>
178 <li><strong>By Chain<br>
179 </strong><em> Assigns a random colour to each PDB chain.</em>
180 <li><strong>Charge & Cysteine<br>
181 </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
182 Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
183 residues in blue.</em></li>
184 <li><strong>Colour with Jmol<br></strong><em>Defers any colouring operations to Jmol. Select this if you want to use the Jmol scripting interface or menu to modify the view directly.</em></li>
185 <li><strong>Standard and User Defined Jalview
187 </strong><em>The remaining entries apply the colourschemes available from
188 the standard and user defined <a href="../colourSchemes/index.html">amino
189 acid colours</a>.</em></li>
193 </strong><em>This pulldown menu is only displayed if there are multiple
194 structures shown in the Jmol window, and Jalview can also locate at
195 least two of the structures in the currently associated alignment view.</em>
197 <li><strong><a name="sAlign">Align</a> <br>
198 </strong><em> When selected, the associated alignment will be used to
199 superimpose all the structures in the view onto the first structure in
200 the alignment. The regions used to calculate the superposition will be
201 highlighted using the 'Cartoon' rendering style, and the remaining
202 data shown as a chain trace.<br>
203 (This option was introduced in Jalview 2.6)</em></li>
209 <li><strong>Jmol Help<br>
210 </strong><em>Access the Jmol Help documentation in a new browser window.</em></li>
215 <p><strong>Functionality provided by Jmol</strong></p>
216 <p>Jmol's own functions are accessed by clicking the 'Jmol' logo or
217 right-clicking in the structure display area. Either way will open the
218 Jmol pop-up menu, which provides access to a number of features for
219 controlling the colour and display of molecules, adding measurements and
220 labels, plotting surfaces, and display animation. The 'Set Picking' menu
221 controls the behaviour of single and double mouse clicking on the
222 structure, and the 'Console' option opens the Jmol scripting console.</p>
223 <p>The state of each Jmol display is stored within <a
224 href="jalarchive.html">jalview archives</a> as a Jmol state recovery
225 script file. This means that any Jmol visualization effects that you add
226 beyond those provided by Jalview will be able to be stored and recovered
227 along with the displayed alignments in Jalview.</p>
228 <p><strong>More Information</strong></p>
229 <p>Jmol is a sophisticated program in its own right, with its own
230 command console and scripting language. Only the essentials have been
231 described here - the interested reader is referred to <a
232 href="http://jmol.sourceforge.net/docs/">Jmol's own comprehensive
233 online documentation</a>.</p>