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:

• hand-controller buttons in ChimeraX virtual reality (details...)
• the right mouse button (= trackpad + Alt on Windows, trackpad + on Mac) in the ChimeraX graphics window

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

The icon for the current right-mouse assignment is highlighted in the Toolbar. A specific mouse button can only be assigned one function at a time.

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

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Tape Measure

The tape measure mouse mode creates one or more pairs of markers with a distance label on the link between them. Clicking (without releasing) the assigned button over volume data, an atom, cartoon, or molecular surface anchors the measurement; dragging adjusts the measurement dynamically, and releasing the button places the second marker. The release point can be anywhere, even empty space. Except in VR, clicking the assigned button in empty space or clicking and releasing without dragging more than 5 screen pixels removes the measurements.

Except in VR, the method of marker placement depends on what is “under” the cursor when the assigned button is clicked or released:

• for volume data, the method is automatically determined from the display style, marking either the isosurface, volume plane, or local maximum along the line of sight
• for an atom, placement is at the atomic center
• for cartoon, placement is at the corresponding residue's principal atom: amino acid CA or nucleic acid C4'
• for molecular surface, placement is at the corresponding atom
• for release over empty space, dragging is simply in the plane of the screen, retaining the same depth as the anchor point

The markers and links are created as a model named tape measure. The link radius is set to 25% of the minimum grid spacing if/when a measurement is anchored on volume data, otherwise remaining at 0.1 Å, and the distance label height is set to 10% of the distance but no less than the link diameter. Label height and color can be changed with the label command, and marker/link radius and color changed with Marker Placement or the marker change command.

Tape-measure differences in virtual reality:

• marker placement is always at the tip of the hand-controller cone, regardless of the data or its style of display
• clicking and releasing within 0.3 seconds erases the measurements
• link radius is not adjusted for volume grid spacing

See also: Distances, measurements

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OpenMM Dynamics

To work with the tug or minimize mouse modes, the entire atomic model must be parametrized in OpenMM, meaning that the structure:

1. must be fully protonated (have all hydrogen atoms present). Hydrogen atoms can be added beforehand with Add Hydrogens or the command addh.
2. must contain only standard residues and water, unless the TugLigands bundle, which contains parameters for >21K additional residue types, has been installed from the ChimeraX Toolshed.

The tug mode runs dynamics on the entire atomic model. 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. These mousemodes use a variable time step Langevin integrator with tolerance 0.001, temperature 100K, nonbonded cutoff 10 Å, and 10 time steps between coordinate updates, with energy minimization occurring automatically 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.

Users may wish to save a session before using either of these mouse modes, since the resulting changes in structure cannot be reversed with undo or by restoring a previously saved view .

See also: tug, minimize, Minimize Structure

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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. Cutoff distances from the clicked residue are initially 5, 4, and 8 Å for residue atoms, residue labels, and map displays, respectively, but can be increased/decreased in increments of 30% by dragging up/down with the assigned button. These zoning actions are implemented via the zone command, which can also be used to adjust zone size. Other parameters such as label color can be changed with zone setting. See also: surface zone, volume zone (with newMap false), select zone, zone atom specification

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Windowing

The windowing mode adjusts volume data image display thresholds collectively: vertical motion adjusts window level (moves all thresholds in parallel to higher or lower values) and 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.

A single transfer function (set of thresholds for an image display) may contain multiple windows, where each window contains one or more thresholds with vertical values above zero and is separated horizontally from other windows by at least two thresholds at the vertical zero. The chest preset is an example of this situation. The windowing mode initially applies to the leftmost window. Click-release of the assigned button without dragging switches the target of this mode to the next window (going from left to right), eventually wrapping around from the rightmost to the leftmost. Any changes in window level and width are limited by “bumping” into a neighboring window.

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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. Some of the mouse modes are modified in VR:

• the zoom mode scales the scene about the position of the hand-controller cone tip (or the two-cone midpoint if zooming with a two-handed gesture) if that point is inside the scene bounding box, otherwise the center of the scene bounding box. Outside of VR, zooming moves the camera toward or away from the scene.
• in select mode, vertical drag broadens/narrows the selection (navigates the selection cascade like using the keyboard up and down arrow keys)
• the label mode makes labels
  yellow
  and reorients them only upon a 45° change in viewing angle rather than continuously
• the zone mode does not turn on ribbon (cartoon) display
• rotate and translate are a single mode in VR
• rotate slab both rotates and translates the volume-data slice in tilted slab image mode
• in crop mode, only the direction of pointing (not the pointer tip coordinates) controls which box face to drag. Pointing at the outside of a volume face will move that face, whereas pointing away from that face will move the opposing parallel face. In other words, the hand-controller moves the box face with normal vector opposite to the direction of pointing. This allows dragging any face of the box in VR without having to rotate the box or move around it. By contrast, in desktop mode, the closest face under the cursor is dragged.