The Jmol PDB Viewer

The interactive structure viewing window is opened by selecting the "Sequence→View PDB entry:" entry in the sequence id pop-up menu. This can only be done for sequences which have an associated PDB structure.

Since Jalview 2.3, Jmol has been integrated into Jalview. It is automatically used by the application, and should also run in the applet in all latest web browsers. If jmol is not available, then the original internal pdb viewer will be used as a fallback.

Controls

The structure is by default rendered as a ribbon diagram. Moving the mouse over the structure brings up tooltips giving the residue name, PDB residue number and chain code, atom name and number ([RES]Num:Chain.AtomName#AtomNumber). If a mapping exists to a residue in any associated sequences, then this will be highlighted in each one's alignment window. The converse also occurs - moving the mouse over an associated residue in an alignment window highlights the associated atoms in the displayed structures.

Selecting a residue highlights its associated sequence residue and alpha carbon location. Double clicking an atom allows distances to be measured from it to any other atom in the structure.

Action	Windows	Unix	Mac/OSX
Rotate View	Left Click and Drag	Left Click and Drag	Click and Drag
Zoom	Shift + Left Click drag mouse up or down	Shift + Left Click or middle button drag mouse up or down	Left-Alt + Click and drag mouse up or down
Select/ Deselect Residue	Left Click	Left Click	Click
Roll View	Shift + Left Click drag mouse to left or right	Shift + Left Click or middle button drag mouse to left or right	Left-Alt + Click and drag mouse to left or right
Move Origin	Shift+Control+Left Click or Middle Button + Drag	Middle-Button and drag	Shift+Control+Left Click or Middle Button and drag
Jmol Menu	Right-Click	Right-Click	Apple-Click

The window has four menus:

• File
  
  • Save As
    Save the displayed PDB File, or 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.
• View
  • Show Chains
    Select which of the PDB file's chains are to be displayed.
• 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.
• Help
  
  • Jmol Help
    Access the Jmol Help documentation in a new browser window.

Functionality provided by Jmol

The Jmol menu provides access to a number of features for controlling the colour and display of molecules, adding measurements and labels, plotting surfaces, and display animation. The 'Set Picking' menu controls the behaviour of single and double mouse clicking on the structure.

The state of each Jmol display is stored within jalview archives as a jmol state recovery script file. This means that any Jmol visualization effects that you add beyond those provided by Jalview will be able to be stored and recovered along with the displayed alignments in Jalview.

More Information

Jmol is a sophisticated program in its own right, with its own command console and scripting language. Only the essentials have been described here - the interested reader is referred to Jmol's own comprehensive online documenation.