3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
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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>
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24 <p>The interactive structure viewing window is opened by selecting
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25 the <strong>"Sequence→View PDB entry:"</strong> entry in
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26 the <a href="../menus/popupMenu.html">sequence id pop-up menu</a>. This
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27 can only be done for sequences which have an <a href="viewingpdbs.html">associated
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29 <p>Since Jalview 2.3, <a href="http://jmol.sourceforge.net/">Jmol</a>
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30 has been integrated into Jalview. It is automatically used by the
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31 application, and should also run in the applet in all latest web
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32 browsers. If jmol is not available, then the original <a
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33 href="pdbviewer.html">internal pdb viewer</a> will be used as a fallback.
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35 <p><strong>Controls</strong></p>
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36 <p>The structure is by default rendered as a ribbon diagram. Moving the
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37 mouse over the structure brings up tooltips giving the residue name,
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38 PDB residue number and chain code, atom name and number
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39 ([RES]Num:Chain.AtomName#AtomNumber). If a mapping exists to a residue
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40 in any associated sequences, then this will be highlighted in each
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41 one's alignment window. The converse also occurs - moving the mouse
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42 over an associated residue in an alignment window highlights the associated
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43 atoms in the displayed structures.</p>
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44 <p>Selecting a residue highlights its associated sequence residue
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45 and alpha carbon location. Double clicking an atom allows distances to
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46 be measured from it to any other atom in the structure.</p>
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50 <td><strong>Action</strong></td>
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51 <td><strong>Windows</strong></td>
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52 <td><strong>Unix</strong></td>
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53 <td><strong>Mac/OSX</strong></td>
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56 <td>Rotate View</td>
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57 <td>Left Click and Drag</td>
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58 <td>Left Click and Drag</td>
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59 <td>Click and Drag</td>
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63 <td>Shift + Left Click<br>drag mouse up or down</td>
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64 <td>Shift + Left Click<br>or middle button<br>drag
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65 mouse up or down</td>
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66 <td>Left-Alt + Click and drag mouse up or down</td>
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78 <td>Shift + Left Click<br>drag mouse to left or
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80 <td>Shift + Left Click<br>or middle button<br>drag mouse to left or right</td>
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81 <td>Left-Alt + Click and drag mouse to left or right</td>
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84 <td>Move Origin</td>
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85 <td>Shift+Control+Left Click<br>or Middle Button<br>
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87 <td>Middle-Button<br>and<br>drag</td>
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88 <td>Shift+Control+Left Click<br>or Middle Button<br>
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93 <td>Right-Click</td>
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94 <td>Right-Click</td>
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95 <td>Apple-Click</td>
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99 <p>The window has four menus:
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101 <li><Strong>File<br>
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104 <li><strong>Save As<br>
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105 </strong><em>Save the displayed PDB File, or the current view as an EPS or PNG file.</em></li>
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106 <li><strong>View Mapping<br>
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107 </strong><em> Opens a text window showing the alignment between the
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108 residues corresponding to alpha-carbon atoms in the PDB structure and
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109 the residues in the associated sequence.</em></li>
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112 <li><strong>View</strong>
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114 <li><strong>Show Chains<br></strong><em>Select which of the PDB
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115 file's chains are to be displayed.</em>
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118 <li><strong>Colours<br>
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121 <li><strong>By Sequence<br>
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122 </strong><em> Colours each residue in the structure with the colour of its
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123 corresponding residue in the associated sequence as rendered in the
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124 associated alignment view, including any Uniprot sequence features or
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125 region colourings.<br>
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126 Residues which only exist in the PDB structure are coloured white if
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127 they are insertions (relative to the associated sequence in the
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128 alignment) and grey if they are N or C terminal flanks outside the
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129 region mapped to the alignment window's sequence.</em></li>
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130 <li><strong>By Chain<br>
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131 </strong><em> Assigns a random colour to each PDB chain.</em>
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132 <li><strong>Charge & Cysteine<br>
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133 </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
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134 Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
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135 residues in blue.</em></li>
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136 <li><strong>Standard and User Defined Jalview
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138 </strong><em>The remaining entries apply the colourschemes available from the
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139 standard and user defined <a href="../colourSchemes/index.html">amino
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140 acid colours</a>.</em></li>
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143 <li><strong>Help<br></strong><ul><li><strong>Jmol Help<br></strong><em>Access the Jmol Help
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144 documentation in a new browser window.</em>
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149 <p><strong>Functionality provided by Jmol</strong>
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150 </p><p>The Jmol menu provides access to a number of features for
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151 controlling the colour and display of molecules, adding measurements and
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152 labels, plotting surfaces, and display animation. The 'Set Picking'
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153 menu controls the behaviour of single and double mouse clicking on the
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155 <p>The state of each Jmol display is stored within <a
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156 href="jalarchive.html">jalview archives</a> as a jmol state recovery script
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157 file. This means that any Jmol visualization effects that
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158 you add beyond those provided by Jalview will be able to be stored and
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159 recovered along with the displayed alignments in Jalview.
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160 </p><p><strong>More Information</strong>
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161 </p><p>Jmol is a sophisticated program in its own right, with its own
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162 command console and scripting language. Only the essentials have been
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163 described here - the interested reader is referred to
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164 <a href="http://jmol.sourceforge.net/docs/">Jmol's own comprehensive
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165 online documenation</a>.</p></p>
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