X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fchimera.html;h=68ac4652fbb80e0ba7aeb611ec0ec42e0161a224;hb=e502a7571bf01a0354ce8205948dd7a3cda1603b;hp=0569513bf0fe2d32e64e26afdf03836f8bfd4d61;hpb=d0771875f23ab994c4f85fb6cd604378768df10e;p=jalview.git

diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index 0569513..68ac465 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">
@@ -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>
@@ -221,10 +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>
@@ -237,8 +258,8 @@
   </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