3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
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4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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6 * This file is part of Jalview.
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8 * Jalview is free software: you can redistribute it and/or
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9 * modify it under the terms of the GNU General Public License
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10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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12 * Jalview is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty
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14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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15 * PURPOSE. See the GNU General Public License for more details.
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17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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20 <title>The Jmol PDB Viewer</title>
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23 <p><strong>The Jmol PDB Viewer</strong></p>
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24 <p>Since Jalview 2.3, <a href="http://jmol.sourceforge.net/">Jmol</a>
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25 has been integrated into Jalview for interactively viewing structures
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26 opened by selecting the <strong>"Sequence→View PDB
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27 entry:"</strong> option in the <a href="../menus/popupMenu.html">sequence
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28 id pop-up menu</a> (if you can't see this, then you need to <a
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29 href="viewingpdbs.html">associate a PDB structure</a> with the
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30 sequence). Jmol is available from the Jalview desktop and should also
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31 run in the JalviewLite applet, providing the browser supports Java 1.5.
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32 If Jmol is not available, then the original <a href="pdbviewer.html">internal
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33 pdb viewer</a> will be used as a fallback.</p>
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34 <p><a name="align"><strong>Superposing structures based
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35 on their aligned sequences</strong></a><br>
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36 If several structures are available on the alignment, you may add
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37 additional structures to an existing Jmol view by selecting their entry
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38 in the appropriate pop-up menu. Jalview will ask you if you wish to add
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39 the structure to the existing alignment, and if you do, it will import
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40 and superimpose the new PDB file using the corresponding positions from
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41 the alignment. If the alignment is subsequently edited, you can use the
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42 <a href="#sAlign"><em>Jmol→Align</em></a> menu option from the
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43 menu bar of the structure view window to superpose the structures using
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44 the updated alignment.<br>
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45 <em>Sequence based structure superposition was added in Jalview 2.6</em>
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47 <p><strong>Controls</strong><br>
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48 The structure is by default rendered as a ribbon diagram. Moving the
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49 mouse over the structure brings up tooltips giving the residue name, PDB
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50 residue number and chain code, atom name and number
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51 ([RES]Num:Chain.AtomName#AtomNumber). If a mapping exists to a residue
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52 in any associated sequences, then this will be highlighted in each one's
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53 alignment window. The converse also occurs - moving the mouse over an
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54 associated residue in an alignment window highlights the associated
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55 atoms in the displayed structures.</p>
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56 <p>Selecting a residue highlights its associated sequence residue
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57 and alpha carbon location. Double clicking an atom allows distances to
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58 be measured from it to any other atom in the structure.</p>
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62 <td><strong>Action</strong></td>
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63 <td><strong>Windows</strong></td>
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64 <td><strong>Unix</strong></td>
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65 <td><strong>Mac/OSX</strong></td>
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68 <td>Rotate View</td>
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69 <td>Left Click and Drag</td>
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70 <td>Left Click and Drag</td>
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71 <td>Click and Drag</td>
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75 <td>Shift + Left Click<br>
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76 drag mouse up or down</td>
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77 <td>Shift + Left Click<br>
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78 or middle button<br>
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79 drag mouse up or down</td>
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80 <td>Left-Alt + Click and drag mouse up or down</td>
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92 <td>Shift + Left Click<br>
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93 drag mouse to left or right</td>
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94 <td>Shift + Left Click<br>
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95 or middle button<br>
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96 drag mouse to left or right</td>
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97 <td>Left-Alt + Click and drag mouse to left or right</td>
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100 <td>Move Origin</td>
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101 <td>Shift+Control+Left Click<br>
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102 or Middle Button<br>
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104 <td>Middle-Button<br>
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107 <td>Shift+Control+Left Click<br>
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108 or Middle Button<br>
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113 <td>Right-Click</td>
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114 <td>Right-Click</td>
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115 <td>Apple-Click</td>
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119 <p>The window has up to five menus:
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121 <li><Strong>File<br>
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124 <li><strong>Save As<br>
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125 </strong><em>Save the displayed PDB File, or the current view as an EPS or
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126 PNG file.</em></li>
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127 <li><strong>View Mapping<br>
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128 </strong><em> Opens a text window showing the alignment between the
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129 residues corresponding to alpha-carbon atoms in the PDB structure and
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130 the residues in the associated sequence.</em></li>
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133 <li><strong>View</strong>
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135 <li><strong>Show Chains<br>
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136 </strong><em>Select which of the PDB file's chains are to be displayed.</em></li>
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138 <li><strong>Colours<br>
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141 <li><strong>By Sequence<br>
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142 </strong><em> Colours each residue in the structure with the colour of its
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143 corresponding residue in the associated sequence as rendered in the
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144 associated alignment view, including any Uniprot sequence features or
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145 region colourings.<br>
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146 Residues which only exist in the PDB structure are coloured white if
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147 they are insertions (relative to the associated sequence in the
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148 alignment) and grey if they are N or C terminal flanks outside the
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149 region mapped to the alignment window's sequence.</em></li>
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150 <li><strong>By Chain<br>
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151 </strong><em> Assigns a random colour to each PDB chain.</em>
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152 <li><strong>Charge & Cysteine<br>
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153 </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
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154 Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
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155 residues in blue.</em></li>
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156 <li><strong>Standard and User Defined Jalview
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158 </strong><em>The remaining entries apply the colourschemes available from
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159 the standard and user defined <a href="../colourSchemes/index.html">amino
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160 acid colours</a>.</em></li>
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163 <li><strong>Jmol<br>
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164 </strong><em>This pulldown menu is only displayed if there are multiple
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165 structures shown in the Jmol window, and Jalview can also locate at
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166 least two of the structures in the currently associated alignment view.</em>
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168 <li><strong><a name="sAlign">Align</a> <br>
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169 </strong><em> When selected, the associated alignment will be used to
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170 superimpose all the structures in the view onto the first structure in
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171 the alignment. The regions used to calculate the superposition will be
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172 highlighted using the 'Cartoon' rendering style, and the remaining
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173 data shown as a chain trace.<br>
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174 (This option was introduced in Jalview 2.6)</em></li>
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177 <li><strong>Help<br>
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180 <li><strong>Jmol Help<br>
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181 </strong><em>Access the Jmol Help documentation in a new browser window.</em></li>
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186 <p><strong>Functionality provided by Jmol</strong></p>
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187 <p>Jmol's own functions are accessed by clicking the 'Jmol' logo or
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188 right-clicking in the structure display area. Either way will open the
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189 Jmol pop-up menu, which provides access to a number of features for
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190 controlling the colour and display of molecules, adding measurements and
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191 labels, plotting surfaces, and display animation. The 'Set Picking' menu
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192 controls the behaviour of single and double mouse clicking on the
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193 structure, and the 'Console' option opens the Jmol scripting console.</p>
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194 <p>The state of each Jmol display is stored within <a
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195 href="jalarchive.html">jalview archives</a> as a Jmol state recovery
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196 script file. This means that any Jmol visualization effects that you add
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197 beyond those provided by Jalview will be able to be stored and recovered
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198 along with the displayed alignments in Jalview.</p>
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199 <p><strong>More Information</strong></p>
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200 <p>Jmol is a sophisticated program in its own right, with its own
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201 command console and scripting language. Only the essentials have been
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202 described here - the interested reader is referred to <a
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203 href="http://jmol.sourceforge.net/docs/">Jmol's own comprehensive
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204 online documentation</a>.</p>
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git://source.jalview.org / jalview.git / blob