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. Once a 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 PDB viewer help page 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 Sequence", and one of the submenus:

- From File - You can load a PDB file from the local machine or network and associate it with the selected sequence. PDB files associated in this way will also be saved in the Jalview Archive file.
- Enter PDB Id - Jalview will use WSDBFetch, provided by the EBI, to fetch the PDB file with the entered Id.
- Discover PDB Ids - Jalview uses the sequence's ID to query WSDBFetch, provided by the EBI, and any enabled DAS servers, to discover PDB ids associated with the sequence.

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.

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.