The Chimera and ChimeraX Viewers

Since Jalview 2.8.2, Chimera ( can be used for viewing structures opened via the "View Structure Data.." dialog. In Jalview 2.11.2, support was also added for ChimeraX, and Pymol.

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 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:

Chimera and Windows Firewall

Jalview and Chimera communicate using Chimera's REST service (
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.