+</li>\r
+<li><strong>Colours<br></strong><ul>\r
+<li><strong>By Sequence<br></strong><em>\r
+Colours each residue in the structure with the colour of its\r
+corresponding residue in the associated sequence as rendered in the\r
+alignment window, including any Uniprot sequence features or region\r
+colourings.<br>Residues which only exist in the PDB structure are\r
+coloured white if they are insertions (relative to the associated\r
+sequence in the alignment) and grey if they are N or C terminal\r
+flanks outside the region mapped to the alignment window's sequence.</em></li>\r
+<li><strong>By Chain<br></strong><em>\r
+Assigns a random colour to each PDB chain.</em>\r
+<li><strong>Charge & Cysteine<br></strong><em>\r
+Highlights cysteines in yellow, anionic (Aspartic Acid or Glutamic Acid) residues in red, and\r
+cationic (Lysine or Arginine) residues in blue.</em>\r
+</li>\r
+<li><strong><em>Standard and User Defined Jalview colourschemes.<br></em></strong>\r
+The remaining entries apply the colourschemes available from the\r
+standard and user defined <a href="../colourSchemes/index.html">amino acid colours</a>.</em>\r
+</li>\r
+</ul>\r
+</li>\r
+<li><strong>View<br></strong><em>\r
+These options can be turned off to improve performance when viewing\r
+large structures, some at the expense of visual clarity.</em><ul>\r
+<li><strong>Wireframe<br></strong><em>\r
+Draws thin lines rather than thick lines for the\r
+alpha-carbon trace.</em>\r
+</li><li><strong>Depthcue<br></strong><em>Shades the structure so parts of the structure near\r
+the front of the view are brighter than those further away.</em>\r
+</li><li><strong>Z Buffering<br></strong><em>\r
+Applies depth sorting to correctly render occluded regions of the\r
+backbone trace.</em>\r
+</li>\r
+<li><strong>Show All Chains<br></strong><em>\r
+When turned on, shows all chains in the PDB file, not just the one\r
+associated with a sequence in the alignment window.</em>\r
+</li>\r
+</ul>\r
+</li>\r
+</ul>\r
+</p>\r
+<p><strong>Notes for PDB Viewing in the Jalview Applet</strong>\r
+<p>The applet can only load PDB files by copying and pasting the text into \r