The Jmol PDB Viewer

Since Jalview 2.3, Jmol has been integrated into Jalview for interactively viewing structures opened by entries in the "Structure" submenu in the sequence id pop-up menu (if you can't see this, then you need to associate a PDB structure with the sequence). Jmol is available from the Jalview desktop and should also run in the JalviewLite applet, providing the browser supports Java 1.5. If Jmol is not available, then the original internal pdb viewer will be used as a fallback.

Superposing structures based on their aligned sequences
If several structures are shown in a view, you can superimpose them using the corresponding positions from the alignment via the Jmol→Align menu option from the menu bar of the structure view window.
Sequence based structure superposition was added in Jalview 2.6

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. Press B or use Select→Select Highlighted columns from any linked alignment window to mark the columns highlighted after mousing over the structure.

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 up to five 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.
  • Ligands
    When available, allows the display of all, none or specific ligands (also known as HETATM groups) in the Jmol view, using CPK spacefilling.
  • Colour by ..
    Submenu allowing specific alignment views to be selected for colouring associated chains in the structure display. This menu contains all the alignment views associated with the structure view, with those used to colour the view indicated by ticks. Addditionally, it contains the following menu entries:
    • Select many views
      When this option is enabled, selecting an alignment view adds it to the set used to colour the structures. Use this when colouring structures related to a number of alignments involving different domains or chains which are shown in the same structure view.
    • Select all views
      This is only enabled when Select many views is also enabled, and will add all associated views to the set used to colour the structure display.
    • Invert selection
      This is only enabled when Select many views is also enabled, and will replace the current set of views with any remaining views not currently used to colour the structure display.
• 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 views, including any UniProt sequence features or region colourings.
    Pick which of the associated alignment views are used to colour the structures using the View→Colour by .. sub menu.
    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.
  • Colour with Jmol
    Defers any colouring operations to Jmol. Select this if you want to use the Jmol scripting interface or menu to modify the view directly.
  • Standard and User Defined Jalview colourschemes.
    The remaining entries apply the colourschemes available from the standard and user defined amino acid colours.
• Jmol
  This pulldown menu is only displayed if there are multiple structures shown in the Jmol window, and Jalview can also locate at least two of the structures in the currently associated alignment view.
  • Align
    When selected, the associated alignment will be used to superimpose all the structures in the view onto the first structure in the alignment. The regions used to calculate the superposition will be highlighted using the 'Cartoon' rendering style, and the remaining data shown as a chain trace.
    (This option was introduced in Jalview 2.6)
• Help
  
  • Jmol Help
    Access the Jmol Help documentation in a new browser window.

Functionality provided by Jmol

Jmol's own functions are accessed by clicking the 'Jmol' logo or right-clicking in the structure display area. Either way will open the Jmol pop-up menu, which 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, and the 'Console' option opens the Jmol scripting console.

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 documentation.