Viewing PDB Structures

Jalview has a simple 3D structure viewer which can visualize polypeptide backbone structures associated with a sequence in a particular alignment view. It is accessed via the "Sequence→View PDB entry:" entry from the sequence's pop-up menu.

To associate PDB files with a sequence, right click on a sequence ID and select "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.

Note: 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).

Sequences which have PDB File associations are annotated with sequence features from the group 'PDBFile' giving 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.

See the PDB Viewer help page for more information.