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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
+ 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
+ for display from the available structures for a sequence.
+
+ - The "Structure→View all N
+ structures
+ option will open a new window containing all structures associated
+ 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
+ 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
+
+
-Jalview can view protein structures associated with a sequence
-via the "Structure→View PDB entry:" entries from a
-sequence's pop-up menu. Once a pdb
+
If a single pdb
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.
-
- Opening structures associated with the current selection
- If one or more of the sequences in the alignment are selected, then
- the Structure submenu of the Sequence
- ID popup menu will contain will include either a 'View all X
- structures' entry in the submenu or a 'View structure for Sequence'
- entry. Both these options will open a new Jmol view containing one, or
- all the structures available for all selected sequences, superimposed
- using the currently selected region of the alignment. (This
- capability was added in Jalview 2.7)
-
Associating PDB files with Sequences
To associate PDB files with a sequence, right click on a sequence
ID and select "Structure→ Associate Structure with