Viewing PDB Structures
Jalview has a simple 3D structure viewer which can load PDB files and associate
the structure with a sequence in an alignment.
There are 2 ways to load and associate a PDB file into Jalview application.
- Select "Sequence Features" from
the "View" menu. This will attempt to match your sequences with
the Uniprot database first by name, then by sequence. The same process will
make note of any PDB files associated with each sequence.
- Select "Fetch Sequence" from an alignment
window or from the main desktop "File" menu. In the popup window
which appears, select PDB as the database and enter your known PDB id. If
you know which chain you wish to retrieve, append the chain id after a colon
eg 1GAQ:B
Note the applet can only load PDB files by copying and pasting the text into
the popup window which appears when "Show PDB Structure" is selected
after right clicking on a sequence name.
To see a particular structure, right click on a sequence name and from the
popup menu select "Sequence -> View PDB Entry".
The PDB Structure viewer will perform a pairwise alignment of your sequence
and each PDB chain sequence. To view the results of the mapping, select "File
-> View Mapping" from the structure viewer window.
Moving the mouse over the structure will highlight the residue in the alignment
window, and vice versa.
Tips for Viewing Structures
- Colour By Sequence follows the exact colours of the alignment window, including
sequence features. Thus you can easily view Uniprot sequence features, eg
helix or metal binding sites on both the alignment and structure viewer.
- Deselect Colours->Show All Chains in order to view only the mapped chain.
- Use Wireframe, without depthcue, and without Z Buffering in order to accelerate
the rendering of the structure.
- You can save an image of your structure as a PNG or EPS file.