PDB Viewing

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:

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 WSDBFetch, provided by the EBI, to discover PDB ids for all the sequences in the alignment which have valid Uniprot names / accession ids.

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.

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.