The ui command adjusts the user interface (UI):
Several ui subcommands set generic tool-interface preferences.• ui autostart true | false tool-name
• ui dockable true | false tool-name
Whether the tool should start automatically upon subsequent ChimeraX startup; saved in preferences. Can also be adjusted through context menus.
• ui favorite true | false tool-name
Whether panels of the tool should be allowed to reinsert automatically when dragged over the main window, as opposed to remaining separate; initially true for all panels except the Help Viewer; saved in preferences. Can also be adjusted through context menus.
• ui fullscreen true | false
Whether the tool should be listed in the Favorites menu; saved in preferences. Can also be adjusted through context menus.
Make the ChimeraX window fill the screen and hide its title bar. See also: camera, Window preferences, using ChimeraX fullscreen
• ui menubar true | false
The tool command (same as ui tool) shows or hides the user interface of the specified tool. Example:tool show "Side View"See also: Tools menu
• ui statusbar true | false
Show/hide the ChimeraX menu on Windows.
• ui windowfill true | false | toggle
Show/hide the status line.
The ui windowfill command expands/contracts the graphics window within the overall window like the icons:• ui hideFloating true | false | toggle
The ui hideFloating command hides/shows all “floating” (undocked) panels collectively. Shift-Esc is equivalent to ui hideFloating toggle. See also: cycling through windows
The functionkey command (same as ui functionkey) assigns ChimeraX commands to the keyboard function keys. The key can be given as F1, F2, etc., with or without capitalization. The wordlist may contain one or more command(s) and their options, or the word none to remove a previous assignment. If multiple commands are included, they must be separated by semicolons and the entire wordlist enclosed in quotation marks. If no wordlist is given, the key's current function is reported in the Log. If no key is specified, any/all function-key assignments are reported. Function key assignments are saved as preferences. See also: alias, buttonpanel, mousemode• mousemode [ control ] [ alt ] [ command ] [ shift ] [ leftMode function ] [ middleMode function ] [ rightMode function ] [ wheelMode function ] [ pauseMode function ]
The mousemode command (same as ui mousemode) assigns ChimeraX functions to the left, middle, and right mouse buttons, alone and in combination with the modifier keys control, alt, command, and shift. In addition, wheelMode refers to scrolling and pauseMode refers to pausing the cursor over something in the graphics window without clicking any buttons. Multiple modifier keys and multiple “buttons” can be given in a single command, but all specified modifiers apply to all specified buttons. For example, two commands rather than one would be needed to assign functions to control right and alt wheel:mousemode control right 'rotate selected models'
mousemode alt wheel contour
A trackpad or single-button mouse can also be used. Given without arguments, the mousemode command reports the current assignments in the Log. The analogous command for virtual reality hand controllers is vr button.
The right-mouse assignment can also be changed by clicking an icon in the Right Mouse tab of the Toolbar. See also: cofr, device, functionkey, ChimeraX window
The mousemode setting command allows adjusting the speed or sensitivity (default 1) of contour level, zoom, and any of the rotation and translation functions. Specifying a speed but omitting the function adjusts the sensitivity of all applicable modes, whereas entering mousemode setting without arguments reports the current value(s) in the Log. Sensitivity changes do not apply to multitouch gestures, however.
Summary of mouse and trackpad default assignments:
rotate left mouse button trackpad click-drag
Mac: also trackpad 2-finger rotation if multitouch gestures enabled
translate middle mouse button Mac: trackpad + Alt, 3-finger drag if multitouch gestures enabled
Windows: trackpad + Ctrl-Alt
+ Shift switches from rotate to translate and vice versa zoom mouse scroll wheel Mac: trackpad pinch or 4-finger drag if multitouch gestures enabled, otherwise 2-finger drag
Windows: trackpad 2-finger drag
select left mouse button + Ctrl, + Shift to toggle or add to selection trackpad + Ctrl, + Shift to toggle or add to selection
The right mouse button (= trackpad + Alt on Windows, trackpad + on Mac) is also assigned to translate by default, but can be reassigned by clicking an icon in the following tabs of the Toolbar:
- Right Mouse:
- Medical Image (just the last section, which contains a subset of the Right Mouse icons)
Details on the functions are given below. 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.
In commands, the function can be truncated to a unique string. If the string contains spaces, it should be enclosed in quotation marks. Not all functions make sense for a given input mode; for example, only identify object and none are reasonable functions for pauseMode.
(default, if any)
description Right Mouse icon select
select items for subsequent operations, +Shift to toggle or add to selection; see also select rotate
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;
assigned button + Shift switches to translate instead
XY-translate (screen coordinates), except if wheel, Z-translate; see also move;
assigned button + Shift switches to rotate instead
zoom the view (slightly different in VR); see also zoom identify object
show identifying information in balloon, atomic-model chain description (if available) in status line none no assignment translate selected models translate models with any part selected, or if no selection, all models;
assigned button + Shift switches to rotate selected models instead
rotate selected models rotate models with any part selected, or if no selection, all models;
assigned button + Shift switches to translate selected models instead
move picked model translate the model under the mouseclick;
assigned button + Shift switches to rotation instead
translate selected atoms translate any selected atoms, or if no selection, all models;
assigned button + Shift switches to rotate selected atoms instead
rotate selected atoms rotate any selected atoms, or if no selection, all models;
assigned button + Shift switches to translate selected atoms instead
translate xy selected models translate models with any part selected in the XY plane of one model's coordinate system (no choice of which if >1 selected), or if no selection, translate all models in the scene XY plane;
assigned button + Shift switches to rotate z selected models instead
rotate z selected models rotate models with any part selected about the Z axis of one model's coordinate system (no choice of which if >1 selected), or if no selection, rotate all models around the scene Z axis;
assigned button + Shift switches to translate xy selected models instead
pivot set center of rotation to clicked atom, bond, ribbon segment, or surface point; see also cofr distance add distance monitor pseudobond between two successively clicked atoms or remove existing distance monitor; see also distance, label, and the tape measure mode 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, 2D arrow (by dragging either end), or “3D” label color key set color key location and dimensions by clicking and dragging; a previously created color key can be moved by clicking near its center and dragging, but clicking elsewhere will delete the key and start over 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 rotate slab activate tilted slab slicing of volume data (image style only), rotate the slab to adjust the slicing angle; the center of rotation from clicking over the slab is the center of the slab, and from clicking elsewhere is the center of the volume box;
assigned button + Shift translates the slab along its axis; in VR, this mode both rotates and translates the slab
crop volume show volume data outline box and adjust region size by dragging any face; see also volume tape measure click to anchor distance measurement, drag to desired endpoint; click in empty space to “erase” (details...); see also the distance mode 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, with wrapping; see also vseries windowing adjust volume data image 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), and the dominant type of motion wins out; for adjusting multiple windows within a single histogram, see details bond rotation adjust torsion angle (original position not retained) by clicking a bond and dragging vertically; 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 play coordinates drag up/down or left/right to play through the coordinate sets in each displayed trajectory; dragging horizontally the full width of the graphics window (or in VR, 50 cm vertically) plays the whole trajectory 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 next docked click-drag to show the next/previous docked ligand when docking results are open in ViewDockX select add add to selection (do not toggle to deselected if already selected) select subtract subtract from selection (do not toggle to selected if already deselected) select toggle toggle selection status (select if not already selected, deselect if selected) rotate and select click to select, drag to rotate
The following mouse modes pertain to markers and links. See also: Marker Placement
function description Markers icon mark maximum add marker at the nearest local maximum in volume data above the threshold along the line of sight mark plane add marker in single-plane volume display mark surface add marker at the nearest surface point along the line of sight mark center add marker at the geometric center of the clicked surface blob, ignoring other blobs mark point Place marker at the tip of the hand-controller cone in virtual reality link markers select and link successively clicked markers move markers drag marker to reposition resize markers drag to adjust marker/link radii delete markers delete markers and links
A click with a trackpad (touchpad) or single-button mouse is generally interpreted as left click, but can be combined with modifier keys to emulate middle and right:
With Trackpad gestures enabled in the Trackpad preferences, multitouch gestures can also be used on Mac trackpads: two-finger rotation, three-finger translation, pinch-zoom, and four-finger scrolling; with the setting turned off, a two-finger drag is interpreted as scrolling. Either way, if “secondary click” is enabled in the Trackpad system preferences, a two-finger click-and-drag performs the right-button action. Magic Mouse scrolling will not work after a trackpad has been used unless the Trackpad gestures option has been turned off.