Viewing PDB Structures
-Jalview can view protein structures associated with a sequence via the "Structure→View - PDB entry:" entries from a sequence's pop-up menu. This will open an - interactive display of the structure in a new window, or prompt you - to associate the sequence with an existing view of the selected - structure. See the Jmol PDB viewer help page - for more information about the display. -
-To associate PDB files with a sequence, right click on a sequence ID and select - "Structure→ Associate Structure with Sequence", - and one of the submenus:
+ +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 +structure is selected, one of the following will happen:
+ +
+ 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 +Sequence", and one of the submenus:
+Importing PDB Entries or files in PDB format
You can retrieve sequences from the PDB using the Sequence Fetcher. Any sequences retrieved with this
- service are automatically associated with their source database entry. For PDB
- sequences, simply select PDB as the database and enter your known PDB id (appended
- with ':' and a chain code, if desired).
-
Jalview will also read PDB files directly. Simply load in the file
-as you would an alignment file. The sequences of any peptide chains
-will be extracted from the file and viewed in the alignment window.
-
Note for jalview applet users: due to the applet security
-constraints, PDB Files can currently only be imported by cut and paste
-of the PDB file text into the text box opened by the 'From File' entry
-of the structure menu.
+Associating a large number of PDB files to sequences
+in an alignment
It is often the case when working with
+structure alignments that you will have a directory of PDB files, and
+an alignment involving one or more of the structures. If you drag a
+number of PDB files onto an alignment in the Jalview desktop, Jalview
+will give you the option of associating PDB files with sequences that
+have the same filename. This means, for example, you can automatically
+associate PDB files with names like '1gaq.pdb' with sequences that
+have an ID like '1gaq'.
+
Note: This feature was added in Jalview 2.7
+
Note for jalview applet users:
+Due to the applet security constraints, PDB Files can currently only be
+imported by cut and paste of the PDB file text into the text box opened
+by the 'From File' entry of the structure menu.
Viewing the PDB Residue Numbering
Sequences which have PDB entry or PDB file associations are annotated
with sequence features from a group named with the associated PDB
-accession number or file name. Each feature gives the corresponding
-PDB Residue Number for each mapped residue in the seuqence. The
-display of these features is controlled through the
-"View→Sequence Features" menu item
-and the Feature Settings dialog
-box.
Outstanding problem with cut'n'pasted
+files in Jalview 2.6 and Jalview 2.7
+Structures imported via the cut'n'paste dialog box will not be correctly
+highlighted or coloured when they are displayed in structure views,
+especially if they contain more than one PDB structure. See the bug
+report at http://issues.jalview.org/browse/JAL-623 for news on this problem.