The Chimera Viewer

Since Jalview 2.8.2, Chimera (http://www.cgl.ucsf.edu/chimera/) can be used for viewing structures opened via the "View Structure Data.." dialog.

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).
Please make sure your version of Chimera is up to date. Jalview requires at least Chimera version 1.11.1

If you save your Jalview session as a project file, the state of any open Chimera windows will also be saved, and can be reopened by loading the project file on any machine with Chimera installed. Since Jalview 2.9.

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. When residues are selected in the Chimera window, they are highlighted on the alignment.

For comprehensive details of Chimera's commands, refer to the tool's Help menu.

Selecting residues in Jalview from Chimera
When a selection is highlighted in a Jalview window, use the Select→Select Highlighted Region or press B to add the mapped positions to the alignment window's column selection.
Hint: Use your machine's 'switch application' key combination (Alt-Tab on Windows and Linux, Cmd-Tab on OSX) to quickly switch between UCSF Chimera and Jalview before pressing 'B' to select highlighted regions.

Basic screen operations (see Chimera help at 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
Select Residues | Ctrl + Click (and drag to select a region) | Ctrl + Click (and drag) | Ctrl + 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.
  - Write Jalview features
    Selecting this option will create new residue attributes for any features currently visible in the associated alignment views, allowing those positions to be selected and analysed with via Chimera's 'Render by Attribute' tool (found in the Tools submenu called Structure Analysis).
    If you use this option, please remember to select the Refresh Menus option in Chimera's Render by Attribute dialog box in order to see the attributes derived from Jalview sequence features.
  - Fetch Chimera Attributes
    This submenu lists available Chimera residue attributes that can be imported as Jalview features on associated sequences.
    This is particularly useful for transferring quantitative positional annotation. For example, structure similarity for an alignment can be visualised by transferring the local RMSD attributes generated by Chimera's Match->Align tool onto aligned sequences and displayed with a Graduated feature colour scheme.
- Help
  - Chimera Help
    Access the Chimera Help documentation in a new browser window.

Chimera and Windows Firewall

Jalview and Chimera communicate using Chimera's REST service (http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html).
Technically this requires both Chimera and Jalview to open ports on the local network, and this may be blocked by Windows Firewall with a warning message such as
"Windows Firewall has blocked some features of this program" (where the program may be jp2launcher.exe for Jalview Webstart, or java.exe or javaw.exe for the InstallAnywhere version).
To allow Jalview and Chimera to interact, you may need to add permission for the program to communicate over the network. This can be done from the warning dialogue, or in Control Panel, Firewall settings.