Mouse Manipulation of Models

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, using a three-button mouse (although fewer buttons can be workable), models are:

• 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 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 rolling a mouse's scroll wheel or by dragging the small square in the Side View horizontally.
  
  
• 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.
  
  
• Ctrl-right mouse button allows repositioning atom and residue labels (those shown with the Actions... Label menu or the commands label and rlabel). The movement is in the plane of the screen (X/Y), or along Z if the Shift key is also pressed.
  
  
• Placing the mouse cursor close to an atom or bond (without clicking any buttons) will cause the corresponding label information to appear in an atomspec balloon. 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 General preferences.

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.

See also: Movement Mouse Mode, Constrained Move, other input devices

• the A(ctive) checkboxes or activation function buttons in the Model Panel
• the checkboxes under the Command Line
• the command select

On a Mac with a one-button mouse, buttons 2 and 3 can be emulated with the option and (apple) keys, respectively. For example, click-dragging with the option key pressed performs XY-translation (assuming default Mouse preferences). In Mac OS 10.5 (Leopard), emulation of a 3-button mouse is off by default, but can be turned on in the Input section of the X11 preferences.

A two-button mouse is also workable. Starting with the default mappings, if the right button of a two-button mouse is not already performing XY-translation, use the Mouse preferences to reassign XY-translation to button 3. The right button of a two-button mouse should then work for XY-translation, leaving the left button for rotation (the default). Scaling can be performed with the Side View or the command scale instead of with the mouse.

Chimera also supports the 3Dconnexion SpaceNavigator^TM input device. Other 3Dconnexion devices such as the SpaceExplorer^TM 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^TM 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^TM 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)