X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=c342bc9d52e8177101c4782edc736f8ccf4a1d69;hb=f27f81a74bbe1be141d23df8aba578515e3179a2;hp=048f0efd41d7ffc0d9a8b48da56e28d83712001f;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index 048f0ef..c342bc9 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -1,32 +1,48 @@
+ -->
PDB Viewing
Viewing PDB Structures
-
-Jalview can view protein structures associated with a sequence
-via the "Structure→" submenu from a
-sequence's pop-up menu.
-The following menu entries are provided for viewing structure data
+
+ Jalview can view protein structures associated with a sequence via the
+ "Structure→" submenu from a sequence's pop-up menu.
+
+ 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.
+
+ The following menu entries are provided for viewing structure data
- The "Structure→View
Structure→ submenu allows a single PDB structure to be chosen
@@ -45,7 +61,6 @@ sequence's pop-up menu.
The View representative structures option was introduced in
Jalview 2.8.1
-
If a single pdb
@@ -53,19 +68,19 @@ structure is selected, one of the following will happen:
- If no structures are open, then an interactive display of the
- structure will be opened in a new window
+ structure will be opened in a new window.
- If another structure is already shown for the current
alignment, then you will be asked if you want to add and align this structure to the structure in
- the existing view. (new feature in Jalview 2.6)
+ the existing view. (new feature in Jalview 2.6).
- If the structure is already shown, then you will be prompted
to associate the sequence with an existing view of the selected
structure. This is useful when working with multi-domain or multi-chain PDB files.
- See the Jmol
- PDB viewer help page for more information about the display.
+ and Chimera PDB viewer help pages for more information about the display.
Associating PDB files with Sequences
To associate PDB files with a sequence, right click on a sequence