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Tool: Mouse Modes for Right Button

The Mouse Modes for Right Button toolbar provides a series of icons for changing the assignment of the right mouse button (= trackpad + Alt on Windows, trackpad + on Mac). Like other tools, this interface can be opened from the Tools menu (more...).

With the related mousemode command, functions can be assigned to all mouse buttons (not just the right) and to scrolling, alone and in combination with modifier keys. See also: Density Map Toolbar, Graphics Toolbar, Molecule Display Toolbar, Marker Placement, Trackpad preferences, virtual reality

Mouse Modes icon mousemode function
(default assignment, if any)
(control left)
select items for subsequent operations; see also select
(default to toggle selection is shift control left)
XY-rotate (screen coordinates) with cursor in central part of window, Z-rotate with cursor in periphery, except if wheel, Y-rotate only; see also turn, roll
(middle, right)
XY-translate (screen coordinates), except if wheel, Z-translate; see also move
zoom the view; see also zoom
rotate and select click to select, drag to rotate
translate selected models translate models with any part selected
rotate selected models rotate models with any part selected
clip activate and translate front clipping plane, +Alt back plane, +Shift slab (front and back in same direction), +Alt-Shift slab thickness (front and back in opposite directions); if only near/far (fixed-orientation) planes already active, move those instead of front/back (rotatable) planes; see also clip
clip rotate activate and rotate front/back clipping planes; see also clip
distance add distance monitor pseudobond between two successively clicked atoms or remove existing distance monitor; see also distance and label
label label/unlabel clicked atom or ribbon segment with residue name and number (slightly different in VR),
unlabel all residues when background is clicked; see also label
move label move 2D label; see also 2dlabels
(shift right)
set center of rotation to atom; see also cofr
bond rotation adjust torsion angle (original position not retained); see also torsion
contour level adjust volume data threshold level; see also volume
move planes show single plane of clicked volume data if full region shown initially, move plane or slab along its axis to show a different section; see also volume
crop volume show volume data outline box and adjust region size by dragging any face; see also volume
place marker place marker (details...)
play map series play volume series; see also vseries
tug drag atoms and apply OpenMM dynamics while button is held down (details...); original coordinates not retained
minimize jiggle residue and its neighbors with OpenMM dynamics while button is held down (details...); original coordinates not retained
swapaa “mutate” and label the amino acid residue under the mouseclick, with vertical drag cycling through the 20 standard types in arbitrary conformations; original sidechain not retained
zone limit atomic and volume data display to a zone around the clicked residue (details...)
windowing adjust volume data solid display thresholds collectively: vertical motion adjusts window level (moves all thresholds in parallel to higher or lower values), horizontal motion adjusts window width (moves thresholds symmetrically farther apart or closer together); the dominant type of motion wins out, i.e., a diagonal motion will not change both level and width

OpenMM Dynamics

To work with the tug or minimize mouse modes, the entire atomic model must be parametrized in OpenMM. Currently, this requires a fully protonated structure containing only standard residues and/or water. Protons can be added beforehand with the command addh.

The tug mode runs dynamics on the entire structure. A model named Tug arrow is added to show the location and direction of tugging. The minimize mode jiggles the residue under the mouseclick along with other residues within 3 Å of the first. It uses a variable time step Langevin integrator with tolerance 0.001, temperature 100K, and 10 time steps between coordinate updates, with energy minimization if a maximum force is exceeded due to bad geometry. Different models do not “feel” the effects of each other; that is, only intra-model forces apply. No nonbonded cutoff is used.

Zone Around Atoms

The zone mouse mode limits atomic detail and volume data (map) display to a zone around the atoms of the clicked residue. Except in VR, the remaining residues of the same atomic model are shown as a narrow ribbon, and residues in the zone are labeled. Subsequently clicking the background clears the labels, and clicking the background a second time shows all atoms for the whole model. These actions are implemented via the zone command, which can also be used to adjust zone size (cutoff distances from the clicked residue are initially 5, 4, and 8 Å for residue atoms, residue labels, and map displays, respectively). See also: surface zone, volume zone (with newMap false), select zone, zone atom specification

Differences in Virtual Reality (VR)

In virtual reality, mouse modes that normally require clicking on an atom (select, label, etc.) require pointing at the atom with the hand-controller cone and pressing the assigned button. Most modes that normally involve clicking and dragging are operated by clicking and moving the hand controller vertically. The bond rotation mode requires rotating the hand controller.

Clicking the Vive menu button (analogous on other systems) shows the ChimeraX control panel with icons in the headset. Each hand controller has multiple buttons that can be assigned to modes (e.g., Vive trigger, trackpad, and grip), and whichever button is used to click the icon is assigned the corresponding function. Outside of VR, clicking a mouse mode icon only assigns the mode to the right mouse button (= trackpad + Alt on Windows, trackpad + on Mac).

Some of the mouse modes are modified in VR to maintain rapid graphics updates and avoid flickering:

UCSF Resource for Biocomputing, Visualization, and Informatics / February 2019