X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=75a5c9cd32bace353f9e504c84b7ecb72d0de62b;hb=2fec1f5de1ec639826d84b7e20c19b37c2a98d55;hp=c2143a3f8ec58a462aeacd0038869689bce1dcf7;hpb=8bc6bb1e8aaa61bd6f1e63d65c5799263063e582;p=jalview.git
diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index c2143a3..75a5c9c 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -1,32 +1,49 @@
+ -->
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
@@ -38,14 +55,13 @@ sequence's pop-up menu.
with the current selection, superposed according to the currently selected region of the alignment.
This
capability was added in Jalview 2.7
- - The "Structure→View all N
+
- The "Structure→View all N
representative structures
option will open a new window containing exactly one structure per
currently selected sequence.
The View representative structures option was introduced in
Jalview 2.8.1
-
If a single pdb
@@ -53,19 +69,19 @@ 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