Viewing PDB Structures

1. Select the "3D Structure Data..." option from a sequence's pop-up menu to open the Structure Chooser dialog box.
   • If one or more structures exists for the given sequence, the Structure Chooser dialog will open with them listed in the results pane.
   • However, if no structure was found, the Structure Chooser interface will present options for manual association of PDB structures.
2. Selecting Structures
   If structures have been discovered, then some will already be selected according to predefined selection criteria, such as structures with the highest resolution. Use the drop down menu to select structures according to different criteria, or, alternatively, choose structures manually by selecting with the keyboard and mouse.
   • Viewing Cached Structures
     If you have previously downloaded structures for your sequences, they can be viewed by selecting the Cached PDB Entries option from the drop down menu at the top of the dialog box.
3. To view selected structures, click the "View" button.

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.

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.
• 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).
• 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 and Chimera PDB viewer help pages for more information about the display.

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 protein or nucleotide chains will be extracted from the file and viewed in the alignment window.

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 sequence. 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.