help/html/features/pdbviewer.html

   1 <html>
   2 <head>
   3 <title>PDB Viewer</title>
   4 </head>
   5 <body>
   6 <p><strong>The PDB Viewer Window</strong>
   7 <p>This interactive structure viewing window is opened by selecting
   8 the <strong>&quot;Sequence&#8594;View PDB entry:&quot;</strong> entry in
   9 the <a href="../menus/popupMenu.html">sequence id pop-up menu</a>. This
  10 can only be done for sequences which have an <a href="viewingpdbs.html">associated
  11 PDB structure</a>.</p>
  12 <p><strong>Controls</strong></p>
  13 <p>The structure is rendered as an alpha-carbon trace. Moving the
  14 mouse over the structure brings up tooltips with a residue name and PDB
  15 sequence position. If a mapping exists to a residue in the associated
  16 sequence, then this will be highlighted in the associated view in its
  17 alignment window, and vice versa for viewing the coordinates associated
  18 with a particular residue in the sequence in a particular view on the
  19 alignment.</p>
  20 <p>Selecting a residue highlights its associated sequence residue
  21 and alpha carbon location.</p>
  22 <p>
  23 <table>
  24         <tr>
  25                 <td><strong>Action</strong></td>
  26                 <td><strong>Windows</strong></td>
  27                 <td><strong>Unix</strong></td>
  28                 <td><strong>Mac/OSX</strong></td>
  29         </tr>
  30         <tr>
  31                 <td>Select/<br>
  32                 Deselect<br>
  33                 Residue</td>
  34                 <td>Left Click</td>
  35                 <td>Left Click</td>
  36                 <td>Click</td>
  37         </tr>
  38         <tr>
  39                 <td>Rotate View</td>
  40                 <td>Left Click and Drag</td>
  41                 <td>Left Click and Drag</td>
  42                 <td>Click and Drag</td>
  43         </tr>
  44         <tr>
  45                 <td>Roll View</td>
  46                 <td>Right Click and drag</td>
  47                 <td>Right Click and Drag</td>
  48                 <td>TODO</td>
  49         </tr>
  50         <tr>
  51                 <td>Move Origin</td>
  52                 <td>Middle-Button and Drag</td>
  53                 <td>Middle-Button and Drag</td>
  54                 <td>TODO</td>
  55         </tr>
  56         <tr>
  57                 <td>Zoom In</td>
  58                 <td>Up Arrow</td>
  59                 <td>Up Arrow</td>
  60                 <td>Up Arrow</td>
  61         </tr>
  62         <tr>
  63                 <td>Zoom Out</td>
  64                 <td>Down Arrow</td>
  65                 <td>Down Arrow</td>
  66                 <td>Down Arrow</td>
  67         </tr>
  68 </table>
  69 </p>
  70 <p>There are three menus:
  71 <ul>
  72         <li><Strong>File<br>
  73         </strong>
  74         <ul>
  75                 <li><strong>Save As<br>
  76                 </strong><em>Saves the current view as an EPS or PNG file.</em></li>
  77                 <li><strong>View Mapping<br>
  78                 </strong><em> Opens a text window showing the alignment between the
  79                 residues corresponding to alpha-carbon atoms in the PDB structure and
  80                 the residues in the associated sequence.</em></li>
  81         </ul>
  82         </li>
  83         <li><strong>Colours<br>
  84         </strong>
  85         <ul>
  86                 <li><strong>By Sequence<br>
  87                 </strong><em> Colours each residue in the structure with the colour of its
  88                 corresponding residue in the associated sequence as rendered in the
  89                 associated alignment view, including any Uniprot sequence features or
  90                 region colourings.<br>
  91                 Residues which only exist in the PDB structure are coloured white if
  92                 they are insertions (relative to the associated sequence in the
  93                 alignment) and grey if they are N or C terminal flanks outside the
  94                 region mapped to the alignment window's sequence.</em></li>
  95                 <li><strong>By Chain<br>
  96                 </strong><em> Assigns a random colour to each PDB chain.</em>
  97                 <li><strong>Charge &amp; Cysteine<br>
  98                 </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
  99                 Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
 100                 residues in blue.</em></li>
 101                 <li><strong><em>Standard and User Defined Jalview
 102                 colourschemes.<br>
 103                 </em></strong> The remaining entries apply the colourschemes available from the
 104                 standard and user defined <a href="../colourSchemes/index.html">amino
 105                 acid colours</a>.</em></li>
 106         </ul>
 107         </li>
 108         <li><strong>View<br>
 109         </strong><em> These options can be turned off to improve performance when
 110         viewing large structures, some at the expense of visual clarity.</em>
 111         <ul>
 112                 <li><strong>Wireframe<br>
 113                 </strong><em> Draws thin lines rather than thick lines for the
 114                 alpha-carbon trace.</em></li>
 115                 <li><strong>Depthcue<br>
 116                 </strong><em>Shades the structure so parts of the structure near the front
 117                 of the view are brighter than those further away.</em></li>
 118                 <li><strong>Z Buffering<br>
 119                 </strong><em> Applies depth sorting to correctly render occluded regions
 120                 of the backbone trace.</em></li>
 121                 <li><strong>Show All Chains<br>
 122                 </strong><em> When turned on, shows all chains in the PDB file, not just
 123                 the one associated with a sequence in the alignment window.</em></li>
 124                 <li><strong>Associate View</strong><br>
 125                 Change which view on the associated sequence's alignment is to be
 126                 associated with the PDB viewer.
 127         </ul>
 128         </li>
 129 </ul>
 130 </p>
 131 <p><strong>Notes for PDB Viewing in the Jalview Applet</strong>
 132 <p>The applet can only load PDB files by copying and pasting the
 133 text into the popup window which appears when &quot;Show PDB
 134 Structure&quot; is selected after right clicking on a sequence name.</p>
 135 </body>
 136 </html>