X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=b1ad4bae86c77cc534a3285c370a2a3e864cb54e;hb=06beaa2f6eb56b94f4dd6408078a14e572cf0eb3;hp=21caca1265fcf7af410635da6e6064fbf74315a9;hpb=dde303bc73617ab4eb3e681e67cf899e6a971318;p=jalview.git
diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index 21caca1..b1ad4ba 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -53,11 +53,12 @@
'highest resolution', simply choose another to pick structures in
a different way.
+ Structure Viewers in the Jalview Desktop
The
+ Jmol viewer has been included since Jalview
+ 2.3. Jalview 2.8.2 included support for Chimera,
+ provided it is installed and can be launched by Jalview. The default
+ viewer can be configured in the Structure
+ tab in the Tools→Preferences dialog box.
+
Structure data imported into Jalview can also be processed to display secondary structure and temperature factor annotation. See the Annotation from Structure page for more information.
+
+
Controlling where the new structures
+ will be shown
+
The Structure Chooser offers several options
+ for viewing a structure.
New View will open a new
+ structure viewer for the selected structures, but if there are views
+ already open, you can select which one to use, and press the Add
+ button. Jalview can automatically superimpose new structures based
+ on the linked alignments - but if this is not desirable, simple
+ un-tick the Superpose Structures checkbox.
+
- If a single PDB structure is selected, one of the
- following will happen:
+ Superposing structures
Jalview superposes structures using
+ the visible portions of any associated sequence alignments. A
+ message in the structure viewer's status bar will be shown if not
+ enough aligned columns were available to perform a superposition.
+ See the Jmol + and Chimera help pages for + more information about their capabilities.
+
Retrieving sequences from the PDB
You can