+ <li><Strong>File<br>
+ </strong>
+ <ul>
+ <li><strong>View Mapping<br>
+ </strong><em> Opens a text window showing the alignment between the
+ residues corresponding to alpha-carbon atoms in the PDB
+ structure and the residues in the associated sequence.</em></li>
+ </ul></li>
+ <li><strong>View</strong>
+ <ul>
+ <li><strong>Show Chains<br>
+ </strong><em>Select which of the PDB file's chains (if more than
+ one) are to be displayed.</em></li>
+ <li><strong>Colour by ..<br></strong><em>Submenu
+ allowing specific alignment views to be selected for
+ colouring associated chains in the structure display. This
+ menu contains all the alignment views associated with the
+ structure view, with those used to colour the view indicated
+ by ticks. Addditionally, it contains the following menu
+ entries:</em>
+ <ul>
+ <li><strong>Select many views<br></strong><em>When
+ this option is enabled, selecting an alignment view adds
+ it to the set used to colour the structures. Use this
+ when colouring structures related to a number of
+ alignments involving different domains or chains which
+ are shown in the same structure view.</em></li>
+ <li><strong>Select all views<br></strong><em>This
+ is only enabled when </em><strong>Select many views</strong><em>
+ is also enabled, and will add all associated views to
+ the set used to colour the structure display.</em></li>
+ <li><strong>Invert selection<br></strong><em>This
+ is only enabled when </em><strong>Select many views</strong><em>
+ is also enabled, and will replace the current set of
+ views with any remaining views not currently used to
+ colour the structure display.</em></li>
+ </ul></li>
+ </ul>
+ <li><strong>Colours<br>
+ </strong>
+ <ul>
+ <li><strong>By Sequence<br>
+ </strong><em> Colours each residue in the structure with the colour
+ of its corresponding residue in the associated sequence as
+ rendered in the associated alignment views, including any
+ UniProt sequence features or region colourings.<br />Pick
+ which of the associated alignment views are used to colour
+ the structures using the <strong>View→Colour
+ by ..</strong> sub menu.
+ </em><br> Residues which only exist in the PDB structure are
+ coloured white if they are insertions (relative to the
+ associated sequence in the alignment) and grey if they are N
+ or C terminal flanks outside the region mapped to the
+ alignment window's sequence.</em></li>
+ <li><strong>By Chain<br>
+ </strong><em>Uses the Chimera 'rainbow chain' command to apply a
+ different colour to each chain.</em></li>
+ <li><strong>Charge & Cysteine<br>
+ </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid
+ or Glutamic Acid) residues in red, and cationic (Lysine or
+ Arginine) residues in blue.</em></li>
+ <li><strong>Colour with Chimera<br></strong><em>Defers
+ any colouring operations to Chimera. Select this if you want
+ to use the Chimera scripting interface or menu to modify the
+ view directly.</em></li>
+ <li><strong>Standard and User Defined Jalview
+ colourschemes.<br>
+ </strong><em>The remaining entries apply the colourschemes available
+ from the standard and user defined <a
+ href="../colourSchemes/index.html">amino acid
+ colours</a>.
+ </em></li>
+ </ul></li>
+ <li><strong>Chimera<br>
+ </strong><em>This pulldown menu is only displayed if there are multiple
+ structures shown in the Chimera window, and Jalview can also
+ locate at least two of the structures in the currently
+ associated alignment view.</em>
+ <ul>
+ <li><strong><a name="sAlign">Align</a> <br> </strong><em>
+ When selected, the associated alignment will be used to
+ superimpose all the structures in the view onto the first
+ structure in the alignment. The regions used to calculate
+ the superposition will be highlighted using the 'Cartoon'
+ rendering style, and the remaining data shown as a chain
+ trace.<br />
+ <br />
+ </em></li>
+ <li><a name="annotxfer"><strong>Write Jalview
+ features</strong></a><br /> <em>Selecting this option will create
+ new residue attributes for any features currently visible in
+ the associated alignment views, allowing those positions to
+ be selected and analysed with via Chimera's 'Render by
+ Attribute' tool (found in the Tools submenu called Structure
+ Analysis).<br /> <br />If you use this option, please
+ remember to select the <em>Refresh Menus</em> option in
+ Chimera's Render by Attribute dialog box in order to see the
+ attributes derived from Jalview sequence features.
+ </em></li>
+ <li><strong>Fetch Chimera Attributes</strong><br /> <em>This
+ submenu lists available Chimera residue attributes that can
+ be imported as Jalview features on associated sequences.<br />This
+ is particularly useful for transferring quantitative
+ positional annotation. For example, structure similarity for
+ an alignment can be visualised by transferring the local
+ RMSD attributes generated by Chimera's Match->Align tool
+ onto aligned sequences and displayed with a <a
+ href="featureschemes.html">Graduated feature colour
+ scheme</a>. </li>
+ </ul></li>
+ <li><strong>Help<br>
+ </strong>
+ <ul>
+ <li><strong>Chimera Help<br>
+ </strong><em>Access the Chimera Help documentation in a new browser
+ window.</em></li>
+ </ul></li>