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.

"Colour by Charge/Cysteine" will colour all Aspartate and Glutamate residues red, Lysine and Arginine will be blue and Cysteine residues will be coloured yellow.

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.
• Use the cursor keys Up and Down arrow to zoom in and zoom out