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:
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.