3 <title>PDB Viewer</title>
6 <p><strong>The Jalview internal PDB Viewer</strong><br>
7 Since Jalview 2.3, the <a href="jmol.html">Jmol PDB Viewer</a> is
8 the main method for <a href="viewingpdbs.html">viewing PDB
9 structures</a>. The documentation below concerns the original Jalview
10 PDB viewer, which is only used in situations where Jmol is unavailable
11 or cannot operate.</p>
12 <p><strong>The PDB Viewer Window</strong>
13 <p>This interactive structure viewing window is opened by selecting
14 the <strong>"Sequence→View PDB entry:"</strong> entry in
15 the <a href="../menus/popupMenu.html">sequence id pop-up menu</a>. This
16 can only be done for sequences which have an <a href="viewingpdbs.html">associated
17 PDB structure</a>, and the PDB Viewer will only be associated with the
18 particular alignment view from which it was opened.</p>
19 <p><strong>Controls</strong></p>
20 <p>The structure is rendered as an alpha-carbon trace. Moving the
21 mouse over the structure brings up tooltips with a residue name and PDB
22 sequence position. If a mapping exists to a residue in the associated
23 sequence, then this will be highlighted in the associated view in its
24 alignment window, and vice versa for viewing the coordinates associated
25 with a particular residue in the sequence in a particular view on the
27 <p>Selecting a residue highlights its associated sequence residue
28 and alpha carbon location.</p>
32 <td><strong>Action</strong></td>
33 <td><strong>Windows</strong></td>
34 <td><strong>Unix</strong></td>
35 <td><strong>Mac/OSX</strong></td>
47 <td>Left Click and Drag</td>
48 <td>Left Click and Drag</td>
49 <td>Click and Drag</td>
53 <td>Right Click and drag</td>
54 <td>Right Click and Drag</td>
59 <td>Middle-Button and Drag</td>
60 <td>Middle-Button and Drag</td>
77 <p>There are three menus:
82 <li><strong>Save As<br>
83 </strong><em>Saves the current view as an EPS or PNG file.</em></li>
84 <li><strong>View Mapping<br>
85 </strong><em> Opens a text window showing the alignment between the
86 residues corresponding to alpha-carbon atoms in the PDB structure and
87 the residues in the associated sequence.</em></li>
90 <li><strong>Colours<br>
93 <li><strong>By Sequence<br>
94 </strong><em> Colours each residue in the structure with the colour of its
95 corresponding residue in the associated sequence as rendered in the
96 associated alignment view, including any Uniprot sequence features or
97 region colourings.<br>
98 Residues which only exist in the PDB structure are coloured white if
99 they are insertions (relative to the associated sequence in the
100 alignment) and grey if they are N or C terminal flanks outside the
101 region mapped to the alignment window's sequence.</em></li>
102 <li><strong>By Chain<br>
103 </strong><em> Assigns a random colour to each PDB chain.</em>
104 <li><strong>Charge & Cysteine<br>
105 </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
106 Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
107 residues in blue.</em></li>
108 <li><strong><em>Standard and User Defined Jalview
110 </em></strong> The remaining entries apply the colourschemes available from the
111 standard and user defined <a href="../colourSchemes/index.html">amino
112 acid colours</a>.</em></li>
116 </strong><em> These options can be turned off to improve performance when
117 viewing large structures, some at the expense of visual clarity.</em>
119 <li><strong>Wireframe<br>
120 </strong><em> Draws thin lines rather than thick lines for the
121 alpha-carbon trace.</em></li>
122 <li><strong>Depthcue<br>
123 </strong><em>Shades the structure so parts of the structure near the front
124 of the view are brighter than those further away.</em></li>
125 <li><strong>Z Buffering<br>
126 </strong><em> Applies depth sorting to correctly render occluded regions
127 of the backbone trace.</em></li>
128 <li><strong>Show All Chains<br>
129 </strong><em> When turned on, shows all chains in the PDB file, not just
130 the one associated with a sequence in the alignment window.</em></li>
131 <!-- NOT YET IMPLEMENTED <li><strong>Associate View</strong><br>
132 Change which view on the associated sequence's alignment is to be
133 associated with the PDB viewer.-->
138 <p><strong>Notes for PDB Viewing in the Jalview Applet</strong>
139 <p>The applet can only load PDB files by copying and pasting the
140 text into the popup window which appears when "Show PDB
141 Structure" is selected after right clicking on a sequence name.</p>