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>
- </ul></li>
- <li><strong>Help<br>
+ <li><strong><a name="experimental">EXPERIMENTAL FEATURES</a></strong><br/>
+ <em>
+ These are only available if the <strong>Tools→Enable
+ Experimental Features</strong> option is enabled. (Since Jalview 2.10.2)</em>
+ <ul>
+ <li><strong>Write Jalview features</strong><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><br />
+ <a href="https://issues.jalview.org/browse/JAL-2295">View
+ this function's issue in Jalview's bug tracker</a></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>.
+ </em><a href="https://issues.jalview.org/browse/JAL-2296">View
+ this function's issue in Jalview's bug tracker</a></li>
+ </ul></li>
+ <li><strong>Help<br>
</strong>
<ul>
<li><strong>Chimera Help<br>