X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=b1ad4bae86c77cc534a3285c370a2a3e864cb54e;hb=06beaa2f6eb56b94f4dd6408078a14e572cf0eb3;hp=f60da1af5b69682a55b3003d93c94af9e37e106a;hpb=08135222cb5e0df30da1d9fb548fccbc7d8ef3fd;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index f60da1a..b1ad4ba 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -56,7 +56,7 @@
- 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 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 @@ -91,42 +90,30 @@ for more information.
- After pressing the
- 'View' button in the Structure Chooser
The behaviour of
- the 'View' button depends on the number of structures selected, and
- whether structure views already exist for the selected structures or
- aligned sequences.
+
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 multiple structures are selected, then Jalview will always create
- a new structure view. The selected structures will be imported into
- this view, and superposed with the matched positions from the
- aligned sequences.
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