<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
number and chain code ([RES]Num:Chain). Moving the mouse over an
associated residue in an alignment window highlights the associated
atoms in the displayed structures. When residues are selected in the
- Chimera window, they are highlighted on the alignment. For
- comprehensive details of Chimera's commands, refer to the tool's
- Help menu.
+ Chimera window, they are highlighted on the alignment.
+ <p>For comprehensive details of Chimera's commands, refer to the
+ tool's Help menu.</p>
+ <p>
+ <strong>Selecting residues in Jalview from Chimera</strong><br />
+ When a selection is highlighted in a Jalview window, use the
+ <em>Select→Select Highlighted Region</em> or press <em>B</em>
+ to add the mapped positions to the alignment window's column
+ selection.<br /> <em>Hint: Use your machine's 'switch
+ application' key combination (Alt-Tab on Windows and Linux,
+ Cmd-Tab on OSX) to quickly switch between UCSF Chimera and Jalview
+ before pressing 'B' to select highlighted regions.</em>
+ </p>
<p>
Basic screen operations (see <a
href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html">Chimera
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>
+ 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>