3 <title>PDB Viewer</title>
6 <p><strong>The PDB Viewer Window</strong>
7 <p>This interactive structure viewing window is opened by selecting
8 the <strong>"Sequence→View PDB entry:"</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>, and the PDB Viewer will only be associated with the
12 particular alignment view from which it was opened.</p>
13 <p><strong>Controls</strong></p>
14 <p>The structure is rendered as an alpha-carbon trace. Moving the
15 mouse over the structure brings up tooltips with a residue name and PDB
16 sequence position. If a mapping exists to a residue in the associated
17 sequence, then this will be highlighted in the associated view in its
18 alignment window, and vice versa for viewing the coordinates associated
19 with a particular residue in the sequence in a particular view on the
21 <p>Selecting a residue highlights its associated sequence residue
22 and alpha carbon location.</p>
26 <td><strong>Action</strong></td>
27 <td><strong>Windows</strong></td>
28 <td><strong>Unix</strong></td>
29 <td><strong>Mac/OSX</strong></td>
41 <td>Left Click and Drag</td>
42 <td>Left Click and Drag</td>
43 <td>Click and Drag</td>
47 <td>Right Click and drag</td>
48 <td>Right Click and Drag</td>
53 <td>Middle-Button and Drag</td>
54 <td>Middle-Button and Drag</td>
71 <p>There are three menus:
76 <li><strong>Save As<br>
77 </strong><em>Saves the current view as an EPS or PNG file.</em></li>
78 <li><strong>View Mapping<br>
79 </strong><em> Opens a text window showing the alignment between the
80 residues corresponding to alpha-carbon atoms in the PDB structure and
81 the residues in the associated sequence.</em></li>
84 <li><strong>Colours<br>
87 <li><strong>By Sequence<br>
88 </strong><em> Colours each residue in the structure with the colour of its
89 corresponding residue in the associated sequence as rendered in the
90 associated alignment view, including any Uniprot sequence features or
91 region colourings.<br>
92 Residues which only exist in the PDB structure are coloured white if
93 they are insertions (relative to the associated sequence in the
94 alignment) and grey if they are N or C terminal flanks outside the
95 region mapped to the alignment window's sequence.</em></li>
96 <li><strong>By Chain<br>
97 </strong><em> Assigns a random colour to each PDB chain.</em>
98 <li><strong>Charge & Cysteine<br>
99 </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
100 Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
101 residues in blue.</em></li>
102 <li><strong><em>Standard and User Defined Jalview
104 </em></strong> The remaining entries apply the colourschemes available from the
105 standard and user defined <a href="../colourSchemes/index.html">amino
106 acid colours</a>.</em></li>
110 </strong><em> These options can be turned off to improve performance when
111 viewing large structures, some at the expense of visual clarity.</em>
113 <li><strong>Wireframe<br>
114 </strong><em> Draws thin lines rather than thick lines for the
115 alpha-carbon trace.</em></li>
116 <li><strong>Depthcue<br>
117 </strong><em>Shades the structure so parts of the structure near the front
118 of the view are brighter than those further away.</em></li>
119 <li><strong>Z Buffering<br>
120 </strong><em> Applies depth sorting to correctly render occluded regions
121 of the backbone trace.</em></li>
122 <li><strong>Show All Chains<br>
123 </strong><em> When turned on, shows all chains in the PDB file, not just
124 the one associated with a sequence in the alignment window.</em></li>
125 <!-- NOT YET IMPLEMENTED <li><strong>Associate View</strong><br>
126 Change which view on the associated sequence's alignment is to be
127 associated with the PDB viewer.-->
132 <p><strong>Notes for PDB Viewing in the Jalview Applet</strong>
133 <p>The applet can only load PDB files by copying and pasting the
134 text into the popup window which appears when "Show PDB
135 Structure" is selected after right clicking on a sequence name.</p>