3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
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4 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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>"Structure→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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137 <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>
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138 <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>
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140 <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>
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142 <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>
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144 <li><strong>Colours<br>
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147 <li><strong>By Sequence<br>
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148 </strong><em> Colours each residue in the structure with the colour of its
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149 corresponding residue in the associated sequence as rendered in the
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150 associated alignment views, including any Uniprot sequence features or
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151 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>
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152 Residues which only exist in the PDB structure are coloured white if
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153 they are insertions (relative to the associated sequence in the
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154 alignment) and grey if they are N or C terminal flanks outside the
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155 region mapped to the alignment window's sequence.</em></li>
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156 <li><strong>By Chain<br>
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157 </strong><em> Assigns a random colour to each PDB chain.</em>
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158 <li><strong>Charge & Cysteine<br>
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159 </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
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160 Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
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161 residues in blue.</em></li>
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162 <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>
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163 <li><strong>Standard and User Defined Jalview
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165 </strong><em>The remaining entries apply the colourschemes available from
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166 the standard and user defined <a href="../colourSchemes/index.html">amino
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167 acid colours</a>.</em></li>
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170 <li><strong>Jmol<br>
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171 </strong><em>This pulldown menu is only displayed if there are multiple
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172 structures shown in the Jmol window, and Jalview can also locate at
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173 least two of the structures in the currently associated alignment view.</em>
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175 <li><strong><a name="sAlign">Align</a> <br>
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176 </strong><em> When selected, the associated alignment will be used to
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177 superimpose all the structures in the view onto the first structure in
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178 the alignment. The regions used to calculate the superposition will be
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179 highlighted using the 'Cartoon' rendering style, and the remaining
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180 data shown as a chain trace.<br>
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181 (This option was introduced in Jalview 2.6)</em></li>
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184 <li><strong>Help<br>
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187 <li><strong>Jmol Help<br>
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188 </strong><em>Access the Jmol Help documentation in a new browser window.</em></li>
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193 <p><strong>Functionality provided by Jmol</strong></p>
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194 <p>Jmol's own functions are accessed by clicking the 'Jmol' logo or
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195 right-clicking in the structure display area. Either way will open the
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196 Jmol pop-up menu, which provides access to a number of features for
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197 controlling the colour and display of molecules, adding measurements and
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198 labels, plotting surfaces, and display animation. The 'Set Picking' menu
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199 controls the behaviour of single and double mouse clicking on the
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200 structure, and the 'Console' option opens the Jmol scripting console.</p>
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201 <p>The state of each Jmol display is stored within <a
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202 href="jalarchive.html">jalview archives</a> as a Jmol state recovery
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203 script file. This means that any Jmol visualization effects that you add
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204 beyond those provided by Jalview will be able to be stored and recovered
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205 along with the displayed alignments in Jalview.</p>
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206 <p><strong>More Information</strong></p>
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207 <p>Jmol is a sophisticated program in its own right, with its own
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208 command console and scripting language. Only the essentials have been
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209 described here - the interested reader is referred to <a
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210 href="http://jmol.sourceforge.net/docs/">Jmol's own comprehensive
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211 online documentation</a>.</p>
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git://source.jalview.org / jalview.git / blob