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).
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.