3D Manipulation

A mouse or touchpad (trackpad) can be used to manipulate the view of structures and other 3-dimensional data in the Chimera graphics window. The Mouse preferences contain assignments for a three-button mouse, but a one- or two-button mouse can also be used. Users of the Mac X11 version of Chimera, see below. See also: Movement Mouse Mode, Constrained Move, other input devices

In the laboratory coordinate system, the X axis is horizontal in the plane of the screen, the Y axis is vertical in the plane of the screen, and the Z axis is perpendicular to the plane of the screen. By default, active models can be:

Also by default, Mouse button assignments and whether to use scrolling can be changed in the Mouse preferences.

Additionally holding down the Shift key reduces the sensitivity to mouse manipulations in the main window and the Side View by a factor of 10.

Users of the Mac X11 version of Chimera on Mac OS 10.5 or higher may need to turn on emulation of a 3-button mouse in the Input section of the X11 preferences. This is not an issue for the native Mac (non-X-Windows) version of Chimera.

Touchpad or One- or Two-Button Mouse

Used alone, a one-button mouse or simple touchpad click-and-drag acts as button 1, but buttons 2 and 3 can be emulated with modifier keys. On a Mac, buttons 2 and 3 can be emulated with the option and command () keys, respectively. For example, touchpad click-and-drag with the option key held down performs the button 2 action, XY-translation by default. See also multitouch actions.

A two-button mouse is also quite workable. The two buttons can be assigned to rotation and (XY) translation, as alternative methods are available for interactive scaling (Side View and possibly scrolling and/or touchpad pinch). Button 1 is already assigned to rotation by default, but depending on whether the other mouse button is treated as button 2 or 3, it may be necessary to use the Mouse preferences to assign it to translation.

An Apple Magic Mouse allows scrolling and can be configured to act as if it had three buttons:

Multi-Touch Actions

Whether to use multitouch gestures on Mac (default true) is specified in the Mouse preferences. On a Mac touchpad, these are:

Activation for Motion

A model must be active (activated for motion) to move in response to manipulations. Models are active by default. Toggling model activation status allows users to manually position one model relative to another. Models can be activated/deactivated using:

Context Menus

Doubleclicking while picking an atom or bond elicits a pop-up menu with entries that depend on the context:

Other Input Devices

See also: RBVI Technology Notes


Chimera supports the 3Dconnexion SpaceNavigatorTM input device. Other 3Dconnexion devices may also work. The 3Dconnexion driver must be installed, except on Linux, where spacenavd (an open-source alternative to the 3Dconnexion driver) must be installed. Thanks to Thomas Margraf, University of Hamburg, for the Linux implementation.

Besides a cap that can be tilted, rotated, and pushed/pulled in any direction, the SpaceNavigator has two buttons with the possible Chimera functions:

The Zoom Direction controls how the cap coordinate system relates to the screen coordinate system: Zoom direction and other settings are shown in system dialogs (for example, the Windows Control Panel or Mac System Preferences), although some of the Mac controls appear to have no effect.

Accelerators (keyboard shortcuts) for changing SpaceNavigator behaviors:

Accelerators are disabled by default. One way to enable their use is with the command ac.

SpaceNavigator problems on Mac:

  1. Chimera responds to SpaceNavigator even when it does not have the application focus.
  2. SpaceNavigator response becomes sluggish after hours of use or idle time.
  3. SpaceNavigator response stops after computer wakes from sleep.
Restarting Chimera resolves problems 2 and 3.

Leap Motion Controller

The Leap Motion Controller uses two cameras to track finger and hand movements. The leap command controls the device's mode of interaction with Chimera.

UCSF Computer Graphics Laboratory / March 2015