Mouse Manipulation of Models
Molecular structures and other 3D data can be manipulated with the mouse
in the Chimera graphics window.
The Mouse preferences
contain assignments for three mouse buttons (1 left, 2 middle, 3 right),
but a touchpad or one- or two-button mouse
can certainly be used. See below
if using the Mac X11 version of Chimera.
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 are:
Also by default,
- rotated with the left mouse button
in the graphics window. Rotation is about the
X and/or Y axis when the cursor is in the central region
of the graphics window (the cursor becomes a small circle) and
about the Z axis when the cursor is in the periphery of the
graphics window (the cursor becomes two curved arrows in yin-yang
configuration). The center of rotation can be adjusted with the
Rotation tool or the command
- XY-translated with the middle mouse button
(the cursor will look like a cross formed by two double-headed arrows).
On Windows, depending on the mouse setup,
an adjustment may be required.
- scaled with the right mouse button (the cursor will look
like a diagonal double-headed arrow enclosing a small square);
movements downward and/or to the right increase the scale,
whereas movements upward and/or to the left decrease it.
Interactive scaling can also be performed by scrolling with the
touchpad or mouse scroll wheel, or by using the
- Z-translated with Ctrl-middle mouse button
(the cursor will look like a vertical double-headed arrow);
movements downward and/or to the right translate
structures closer, and movements upward and/or to the left
translate structures farther away. Note that Z-translation is not the same
Mouse button assignments can be changed in the
- Ctrl-left mouse button performs
(selection from the graphics window);
the cursor will look like a pointing hand.
Doubleclicking while picking an atom or bond elicits a
- Ctrl-right mouse button allows repositioning
atom and residue labels (those shown with the
Actions... Label menu or
the commands label
and rlabel) and
The movement is in the plane of the screen (X/Y), or along Z if
the Shift key is also pressed.
- Pausing the mouse cursor over an atom or bond (without
clicking any buttons) will show the corresponding label information
in an atomspec balloon, and the PDB description of the chain,
if available, in the status line.
Similarly, many dialogs
include balloon help, additional text that is displayed
when the cursor is paused near some relevant part of the dialog.
Whether these balloons should appear can be set in the
Additionally holding down the Shift key reduces the speed
(mouse sensitivity) of manipulations in the main window and
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.
Activation for Motion
A model must be active (activated for motion)
to move in response to mouse 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:
Doubleclicking while picking
an atom or bond elicits a pop-up menu with entries that depend on the context:
- for an atom when 0 or >3 other atoms are
- if the atom is a metal ion, Coordination Geometry
- open the Metal
- Show Distances to Nearby Residues - label and display residues
with any atom within 3.6 Å of the current atom, show the corresponding
(ignoring atoms in the same residue as or within two bonds of the current atom),
remove monitors and labels previously shown for another atom
using this function; toggles to Hide Distances...
to remove monitors and labels previously shown for the current atom
- Modify Atom - open the
- Set Pivot - set fixed
center of rotation
at the atom
- open Selection Inspector
- for an atom when one other atom is selected:
- for an atom when two other atoms are selected:
- for an atom when three other atoms are selected:
- for a bond when no other bonds are selected:
- for a pseudobond, or
for a bond when other bonds are selected:
Touchpad or One- or Two-Button Mouse
Used alone, a touchpad or one-button mouse acts as button 1,
but modifier keys allow emulating buttons 2 and 3.
On a Mac, buttons 2 and 3 can be emulated with the option and
command () keys,
For example, using the touchpad while pressing the option key
performs the button 2 action, XY-translation by default.
Depending on system settings, two-finger scrolling on the touchpad may
A two-button mouse is also quite workable.
The two buttons can be assigned to rotation and (XY) translation,
as alternative approaches are available for interactive scaling
(Side View, mouse scroll wheel
if present, and/or touchpad scrolling).
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.
Other Input Devices
Chimera also supports the
SpaceNavigatorTM input device.
Other 3Dconnexion devices such as the SpaceExplorerTM
may also work.
The 3Dconnexion driver must be installed, except on Linux, where
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:
- Button 1 or Fit centers the models
and scales them to fit in the window
- Button 2 toggles a mode allowing
simultaneous rotation and translation (the default
only allows rotation or translation depending on which user motion
has the larger amplitude)
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.
- when up/down cap motion zooms the models,
the tabletop plane maps to the plane of the screen;
the systems are related by a rotation of approximately 90°
- when closer/farther cap motion zooms the models,
the systems are approximately aligned
(keyboard shortcuts) for changing SpaceNavigator behaviors:
Accelerators are disabled by default. One way to enable their use is
with the command ac.
- na - toggle between moving all models and moving only the
- nd - toggle between dominant mode
and allowing simultaneous rotation and translation
- nf - toggle fly-through mode,
where the device moves the viewpoint rather than the models
(as if all axes were reversed); currently hard to control
- nz - toggle whether model in/out motion is true zooming
(scaling the entire scene) or Z-translation (moving models relative
to the front and back clipping planes)
SpaceNavigator problems on Mac:
Restarting Chimera resolves problems 2 and 3.
- Chimera responds to SpaceNavigator even when it does not have the application focus.
- SpaceNavigator response becomes sluggish after hours of use or idle time.
- SpaceNavigator response stops after computer wakes from sleep.
UCSF Computer Graphics Laboratory / May 2012