X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fchimera.html;h=e1227de7541038ed6ca28ee7d2df0a4eb5ee4c57;hb=0bee8aadc22e41e4793db251a7d37a839bd77db8;hp=39dff7534e127825a20236e777e77df07c4e79bc;hpb=c17661b22323a66090ea91e04751aa17461b17c5;p=jalview.git

diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index 39dff75..e1227de 100644
--- a/help/html/features/chimera.html
+++ b/help/html/features/chimera.html
@@ -28,43 +28,23 @@
   </p>
   <p>
     Since Jalview 2.8.2, <a href="http://www.cgl.ucsf.edu/chimera/">Chimera</a>
-    (http://www.cgl.ucsf.edu/chimera/) has been integrated into Jalview
-    for interactively viewing structures opened by entries in the <strong>&quot;Structure&quot;</strong>
-    submenu in the <a href="../menus/popupMenu.html">sequence id
-      pop-up menu</a> (if you can't see this, then you need to <a
-      href="viewingpdbs.html"
-    >associate a PDB structure</a> with the sequence). Chimera is
-    available from the Jalview desktop, provided Chimera has been
-    separately installed.
+    (http://www.cgl.ucsf.edu/chimera/) can be used for viewing
+    structures opened via the <a href="structurechooser.html"><strong>&quot;View
+        Structure Data..&quot;</strong> dialog</a>.
   </p>
   <p>
     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).
+    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
     open Chimera windows will also be saved, and can be reopened by
     loading the project file on any machine with Chimera installed. <em>Since
       Jalview 2.9.</em>
-    <!-- <p>The following menu entries are provided for viewing structure data<br>
-  <ul>
-    <li>The <strong>&quot;Structure&#8594;View
-        Structure&#8594;</strong> submenu allows a single PDB structure to be chosen
-      for display from the available structures for a sequence.
-    </li>
-    <li>The <strong>&quot;Structure&#8594;View all <em>N</em>
-        structures
-    </strong> option will open a new window containing all structures associated
-      with the current selection.
-    </li>
-    <li>The <strong>&quot;Structure&#8594;View all <em>N</em>
-        representative structures
-    </strong> option will open a new window containing exactly one structure per
-      currently selected sequence.<br /></li>
-  </ul>
-  <br> 
-</p> -->
   <p>
     <a name="align"><strong>Superposing structures based on
         their aligned sequences</strong></a><br> If several structures are
@@ -85,13 +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">
@@ -181,7 +171,7 @@
         </strong><em> Colours each residue in the structure with the colour
             of its corresponding residue in the associated sequence as
             rendered in the associated alignment views, including any
-            Uniprot sequence features or region colourings.<br />Pick
+            UniProt sequence features or region colourings.<br />Pick
             which of the associated alignment views are used to colour
             the structures using the <strong>View&#8594;Colour
               by ..</strong> sub menu.
@@ -205,8 +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>
@@ -221,8 +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>
@@ -237,8 +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