JAL-2629 update spike branch to latest

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

diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index 98d8966..e1227de 100644 (file)
--- a/help/html/features/chimera.html
+++ b/help/html/features/chimera.html
@@ -36,9 +36,9 @@
     You can set a default choice of Jmol or Chimera structure viewer in
     <a href="preferences.html#structure"> Preferences</a>. You can also
     optionally specify the path to the Chimera program here (if it
-    differs from the standard paths searched by Jalview).<br />
-    <strong>Please make sure your version of Chimera is up to
-      date. Jalview requires at least Chimera version 1.11.1</strong>
+    differs from the standard paths searched by Jalview).<br /> <strong>Please
+      make sure your version of Chimera is up to date. Jalview requires
+      at least Chimera version 1.11.1</strong>
   </p>
   <p>
     If you save your Jalview session as a project file, the state of any
@@ -65,13 +65,23 @@
     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 help</a> at
+      href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html">Chimera
+      help</a> at
     http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html
     for full details).
   <table border="1">
@@ -185,8 +195,8 @@
             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>.
+            href="../colourSchemes/index.html">amino acid
+              colours</a>.
         </em></li>
       </ul></li>
     <li><strong>Chimera<br>
@@ -201,8 +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>
@@ -217,8 +249,8 @@
   </p>
   Jalview and Chimera communicate using Chimera's
   <a
-    href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html"
-  >REST service</a>
+    href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html">REST
+    service</a>
   (http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html).
   <br> Technically this requires both Chimera and Jalview to open
   ports on the local network, and this may be blocked by Windows