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:

• 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 cofr.
  
  
• 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 (zoomed) 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 done with the Side View and possibly scrolling.
  
  
• 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 as scaling.

• Ctrl-left mouse button performs picking (selection from the graphics window); the cursor will look like a pointing hand. Doubleclicking while picking an atom or bond elicits a context menu.
  
  
• Ctrl-right mouse button centers a clicked item (atom, bond, pseudobond, residue ribbon, or surface piece) and makes the centered point a fixed center of rotation; clicking empty space restores the front center rotation mode.
  
  
• Pausing the 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. Whether to show atomspec balloons can be set in the Labels preferences. Similarly, many dialogs include balloon help, additional text that is displayed when the cursor is paused near some relevant part of the dialog. Whether to show balloon help can be set in the Messages 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.

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:

• “secondary click” can be enabled in the Mac System Preferences (acts as button 3 in Chimera)
• the free MagicPrefs app can be used to activate middle click (acts as button 2 in Chimera)

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

• two-finger drag - XY-rotation
• two-finger twist - Z-rotation
• pinch motion - zooming (scaling)
• three-finger drag - XY-translation

• the A(ctive) checkboxes or activation function buttons in the Model Panel
• the model-activation checkboxes below the Command Line (shown by default, see the Command Line preferences)
• the command select

• for an atom when 0 or >3 other atoms are selected:
  • if the atom is a metal ion, Coordination Geometry - open the Metal Geometry tool
  • Show Distances to Nearby Residues - label and display residues with any atom within 3.6 Å of the current atom, show the corresponding distance monitors (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 Modify Structure dialog
  • Set Pivot - set fixed center of rotation at the atom
  • Inspect - open Selection Inspector
• for an atom when one other atom is selected:
  • Show Distance - create a distance monitor between the two atoms
  • Inspect - open the Selection Inspector
• for an atom when two other atoms are selected:
  • Measure Angle - show a measurement of the angle formed by the three atoms in the Angles/Torsions dialog
  • Inspect - open the Selection Inspector
• for an atom when three other atoms are selected:
  • Measure Torsion - show a measurement of the torsion angle formed by the four atoms in the Angles/Torsions dialog
  • Inspect - open the Selection Inspector
• for a bond when no other bonds are selected:
  • Rotate Bond - activate the bond for rotation, open the Adjust Torsions dialog
  • Adjust Bond - open the Adjust Bonds dialog to delete the bond or change its length
  • Select Bonded - select the flanking atoms
  • Inspect - open the Selection Inspector
• for a pseudobond, or for a bond when other bonds are selected:
  • Select Bonded - select the flanking atoms
  • Inspect - open the Selection Inspector

• SpaceNavigator
• Leap Motion Controller

See also: RBVI Technology Notes

Chimera supports the 3Dconnexion SpaceNavigator^TM 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:

• 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 dominant mode only allows rotation or translation depending on which user motion has the larger amplitude)

• 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

Accelerators (keyboard shortcuts) for changing SpaceNavigator behaviors:

• na - toggle between moving all models and moving only the active models
• 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:

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.

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.