Viewing PDB Structures
Jalview can be used to view protein structures by following the steps below:Structure data imported into Jalview can also be processed to display secondary structure and temperature factor annotation. See the Annotation from Structure page for more information.
If a single pdb structure is selected, one of the following will happen:
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.