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.
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).
|Rotate View||Left Click and Drag||Left Click and Drag||Left Click and Drag|
drag mouse up or down
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
|Select Residues||Ctrl + Click (and drag to select a region)||Ctrl + Click (and drag)||Ctrl + Click (and drag)|
The Jalview Chimera View window has up to five menus:
Chimera and Windows FirewallJalview and Chimera communicate using Chimera's REST service (http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html).