MagicPrefs has been updated. MM2 is now supported. 3 points 4 years ago. Check the App Store, its amazing. 2 points 4 years ago. MagicPrefs is a free application for OS X which aims to improve the functionality and configuration options of the Apple Magic Mouse, Magic Trackpad and the MacBook glass trackpad.
3D Manipulation
A mouse or touchpad (trackpad) can be used to manipulate theview of structures and other 3-dimensional data in theChimera graphics window.The Mouse preferencescontain 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 thescreen, the Y axis is vertical in the plane of the screen, and theZ axis is perpendicular to the plane of the screen.By default, active models can be:
- rotated with the left mouse buttonin the graphics window. Rotation is about theX and/or Y axis when the cursor is in the central regionof the graphics window (the cursor becomes a small circle) andabout the Z axis when the cursor is in the periphery of thegraphics window (the cursor becomes two curved arrows in yin-yangconfiguration). The center of rotation can be adjusted with theRotation 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 looklike 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 theSide Viewand 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 translatestructures closer, and movements upward and/or to the lefttranslate structures farther away. Note that Z-translation is not the sameas 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 acontext menu.
- Ctrl-right mouse button centers a clicked item(atom, bond, pseudobond, residue ribbon,or surface piece)and makes the centered point afixedcenter of rotation;clicking empty space restores the front centerrotation mode.
- Pausing the cursor over an atom or bond (withoutclicking 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 theLabels 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 theMessages preferences.
Additionally holding down the Shift key reduces the sensitivity tomouse manipulations in the main window and theSide View by a factor of 10.
Users of the Mac X11 version of Chimera on Mac OS 10.5 or highermay need to turn on emulation of a 3-button mousein 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-dragacts 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 downperforms 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 possiblyscrolling and/or touchpad pinch).Button 1 is already assigned to rotation by default, but depending on whetherthe other mouse button is treated as button 2 or 3, it may be necessary to usethe Mouse preferences to assignit 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 freeMagicPrefs app can be used to activate middle click (acts as button 2 in Chimera)
Multi-Touch Actions
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
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:- the A(ctive) checkboxes or activation function buttonsin the Model Panel
- the model-activation checkboxes below theCommand Line(shown by default, see theCommand Line preferences)
- the command select
Context Menus
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 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
Other Input Devices
See also: RBVI Technology Notes
SpaceNavigator
Chimera supports the 3DconnexionSpaceNavigatorTM input device. Other 3Dconnexion devices may also work. The 3Dconnexion driver must be installed, except on Linux, wherespacenavd (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 SpaceNavigatorhas 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 modeonly allows rotation or translation depending on which user motionhas 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
Magicprefs Magic Mouse 2
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:
- 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:
- 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.
Magicprefs For Windows
Leap Motion Controller
Magicprefs Alternative 2020
The Leap Motion Controlleruses two cameras to track finger and hand movements.The leap command controls the device'smode of interaction with Chimera.
UCSF Computer Graphics Laboratory / March 2015