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.

Controls

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
Select/ Deselect Residue	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:

• File
  
  • Save As
    Saves the current view as an EPS or PNG file.
  • View Mapping
    Opens a text window showing the alignment between the residues corresponding to alpha-carbon atoms in the PDB structure and the residues in the associated sequence.
• Colours
  
  • By Sequence
    Colours each residue in the structure with the colour of its corresponding residue in the associated sequence as rendered in the associated alignment view, including any UniProt sequence features or region colourings.
    Residues which only exist in the PDB structure are coloured white if they are insertions (relative to the associated sequence in the alignment) and grey if they are N or C terminal flanks outside the region mapped to the alignment window's sequence.
  • By Chain
    Assigns a random colour to each PDB chain.
  • Charge & Cysteine
    Highlights cysteines in yellow, anionic (Aspartic Acid or Glutamic Acid) residues in red, and cationic (Lysine or Arginine) residues in blue.
  • Standard and User Defined Jalview colourschemes.
    The remaining entries apply the colourschemes available from the standard and user defined amino acid colours.
• View
  These options can be turned off to improve performance when viewing large structures, some at the expense of visual clarity.
  • Wireframe
    Draws thin lines rather than thick lines for the alpha-carbon trace.
  • Depthcue
    Shades the structure so parts of the structure near the front of the view are brighter than those further away.
  • Z Buffering
    Applies depth sorting to correctly render occluded regions of the backbone trace.
  • Show All Chains
    When turned on, shows all chains in the PDB file, not just the one associated with a sequence in the alignment window.

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.