X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fchimera.html;h=e1227de7541038ed6ca28ee7d2df0a4eb5ee4c57;hb=60541afc96ff3a4f5b79b78009922f373cbc29c3;hp=cbef2c1616eaa806888f03702b0bae4b3f6a9710;hpb=936ac942e96e2767e1b1fff46e805e8a1e5be1c7;p=jalview.git

diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index cbef2c1..e1227de 100644
--- a/help/html/features/chimera.html
+++ b/help/html/features/chimera.html
@@ -73,7 +73,10 @@
     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.
+    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
@@ -208,8 +211,30 @@
             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>