The Jalview internal PDB Viewer
Since Jalview 2.3, the Jmol PDB Viewer is the main method for viewing PDB structures. The documentation below concerns the original Jalview PDB viewer, which is only used in situations where Jmol is unavailable or cannot operate.

The PDB Viewer Window

This interactive structure viewing window is opened by selecting entries from the "Structure→" submenu of the sequence id pop-up menu. The internal PDB viewer is not able to show superpositions, so no other options are provided. Structures can only be viewed for sequences which have an associated PDB structure, and the PDB Viewer will only be associated with the particular alignment view from which it was opened.


The structure is rendered as an alpha-carbon trace. Moving the mouse over the structure brings up tooltips with a residue name and PDB sequence position. If a mapping exists to a residue in the associated sequence, then this will be highlighted in the associated view in its alignment window, and vice versa for viewing the coordinates associated with a particular residue in the sequence in a particular view on the alignment.

Selecting a residue highlights its associated sequence residue and alpha carbon location.

Action Windows Unix Mac/OSX
Left Click Left Click Click
Rotate View Left Click and Drag Left Click and Drag Click and Drag
Roll View Right Click and drag Right Click and Drag TODO
Move Origin Middle-Button and Drag Middle-Button and Drag TODO
Zoom In Up Arrow Up Arrow Up Arrow
Zoom Out Down Arrow Down Arrow Down Arrow

There are three menus:

Notes for PDB Viewing in the Jalview Applet

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.