The Chimera Viewer

Since Jalview 2.8.2, Chimera (http://www.cgl.ucsf.edu/chimera/) 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). Chimera is available from the Jalview desktop, provided Chimera has been separately installed.

You can set a default choice of Jmol or Chimera structure viewer in Preferences. You can also optionally specify the path to the Chimera program here (if it differs from the standard paths searched by Jalview).

The following menu entries are provided for viewing structure data

• The "Structure→View Structure→ submenu allows a single PDB structure to be chosen for display from the available structures for a sequence.
• The "Structure→View all N structures option will open a new window containing all structures associated with the current selection.
• The "Structure→View all N representative structures option will open a new window containing exactly one structure per currently selected sequence.
  

Superposing structures based on their aligned sequences

If several structures are available on the alignment, you may add additional structures to an existing Chimera view by selecting their entry in the appropriate pop-up menu. Jalview will ask you if you wish to add the structure to the existing alignment, and if you do, it will import and superimpose the new PDB file using the corresponding positions from the alignment. If the alignment is subsequently edited, you can use the Chimera→Align menu option from the menu bar of the structure view window to superpose the structures using the updated alignment.

Chimera 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 ([RES]Num:Chain). Moving the mouse over an associated residue in an alignment window highlights the associated atoms in the displayed structures. For comprehensive details of Chimera's commands, refer to the tool's Help menu.

Basic screen operations (see Chimera help (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html) for full details).

Action	Windows	Unix	Mac/OSX
Rotate View	Left Click and Drag	Left Click and Drag	Left Click and Drag
Zoom	Right Click drag mouse up or down	Right Click drag mouse up or down	cmd or Right + Click and drag mouse up or down, or use mouse scroll button
Move Origin	Middle Button + Drag	Middle Button and drag	alt + Click and drag

Jalview Controls

The Jalview Chimera View window has up to five menus:

• 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 (if more than one) are to be displayed.
  • 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
    Uses the Chimera 'rainbow chain' command to apply a different colour to each 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 Chimera
    Defers any colouring operations to Chimera. Select this if you want to use the Chimera 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.
• Chimera
  This pulldown menu is only displayed if there are multiple structures shown in the Chimera 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.
    
• Help
  
  • Chimera Help
    Access the Chimera Help documentation in a new browser window.