Viewing PDB Structures

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

There are two ways to associate PDB files with sequences:

• Select "Sequence Features" from the "View" menu, which retrieves any uniprot sequence records associated with the sequences in the alignment. If, for a particular sequence's uniprot record there are any cross-references to PDB structures, then these will be added to its list of associated database ids.
• 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).