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Toolbar: Right Mouse

Icons in the Right Mouse tab of the Toolbar (along with those in the Markers tab) allow reassigning the function or “mouse mode” of:

(On Windows or Linux, right-click elsewhere in the ChimeraX interface raises a context menu.)

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: Marker Placement, Measure and Color Blobs, Map Eraser, Trackpad preferences

icon mousemode function
(default assignment, if any)
(control left)
select items for subsequent operations, +Shift to toggle; see also select
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 (slightly different in VR); see also zoom
translate selected models translate models with any part selected
rotate selected models rotate models with any part selected
pivot set center of rotation to atom; see also cofr
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 or “3D” label; see also 2dlabels, label
clip click without dragging to activate/deactivate clipping, click-drag to activate (if clipping is not yet active) and translate front or near plane, +Alt back or far plane, +Shift slab (translate paired planes in same direction), +Alt-Shift slab thickness (translate paired planes in opposite directions); whether activation applies to front/back planes that rotate with the scene or near/far planes that remain parallel to the screen is set in the Clipping preferences; see also clip
clip rotate click without dragging to activate/deactivate clipping, click-drag to activate (if not already active) and rotate front/back clipping planes; see also clip
zone limit atomic and volume data display to a zone around the clicked residue (details...)
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
pick blobs pick surface blob to measure area, volume, size; see also measure blob
map eraser move map eraser sphere; see also volume erase
play map series play volume series; see also vseries
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
bond rotation adjust torsion angle (original position not retained); see also torsion
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
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

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 clicked residue and labels the residues in the zone. Except in VR, the remaining residues of the same atomic model are shown as a narrow ribbon. Subsequently clicking the background clears the labels, and clicking the background a second time returns to what was shown before the residue was clicked. 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:

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