Merge branch 'develop' into features/JAL-2446NCList

[jalview.git] / help / html / features / chimera.html

diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index 1b0b9c1..68ac465 100644 (file)
--- a/help/html/features/chimera.html
+++ b/help/html/features/chimera.html
@@ -65,9 +65,19 @@
     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&#8594;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
@@ -201,10 +211,41 @@
             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&#8594;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>