Viewer guide

Find a control

Control	Use
Open	Load a file from your desktop
View	Representation, layers, atom size, and periodic display
Edit	Atom coordinates, elements, and cell
Analyze	Atom properties, measurements, and trajectory analysis
Export	Figure dimensions, format, and recipes
Search	Find atoms, settings, and commands

On narrow screens, Tools opens the inspector sheet; its arrow expands it. In short landscape windows, the inspector sits beside the canvas.

Navigate and select

Gesture	Action
Drag	Rotate
Secondary-drag or middle-drag	Pan
Scroll or pinch	Zoom
Click an atom	Select it and open its details
Shift-drag a box	Add a group of atoms
Click empty space	Clear selection

Fit, 3D, XY, XZ, and YZ sit above the canvas. Camera orientation and selection stay stable while frames change. Box selection creates a group; use an ordered selection for geometric measurements.

Measure in order

1. Click the first atom.

2. With Analyze open, press Shift+Tab to focus the molecular canvas.

3. Use ↑ / ↓ to browse atoms, then Enter to add each atom in order. Pressing Enter on a selected atom removes it.

4. Choose Plot to follow the measurement through the trajectory, or Pin to keep it for recall.

Ordered atoms	Measurement
2	Distance (Å)
3	Angle (°)
4	Dihedral (°)

This synthetic water trajectory has the cell hidden. Periodic measurements use the exact minimum image by default; switch to displayed images to measure a chosen replica. Plot cursors follow the displayed frame; clicking a plot point returns to that frame. See trajectory analysis for pair distributions, coordination, and normalization.

One selected atom shows its position and available charge, force, and velocity. Groups show formula, centroid, extent, and unique-atom count. The selection bar offers Select for element, molecule, residue, connected-component, or distance-based groups, and Track for recent atom paths.

Change the display

View offers the representations and layers supported by the source. Unavailable representations explain their requirements on hover, focus, or selection. Periodic cell contains wrapping, centering, and repeats; Rendering controls interactive quality.

Coordination polyhedra depict visible bonding topology, using the nearest distance shell when bonds are inferred. Planar shells become polygons; transition-metal sites are preferred when several metal types are present. Polyhedra protruding outside one displayed cell are omitted; dense structures show a deterministic subset. This display is not a coordination-number analysis.

A single displayed cell omits minimum-image bonds through its boundary. Repeats retain bonds between neighboring displayed cells. Display operations preserve source coordinates; Search → Source coordinates shows stored positions. See cell and wrapping conventions for centred, low-rank, and vacuum cells.

The interactive view uses bundled 3Dmol; if initialization fails, it falls back to the publication renderer. Figure export uses a separate renderer.

Edit the structure

Open Edit or press E.

Edit	Scope
Element identity	Whole structure
Cartesian coordinates	Displayed frame
Cell lengths/angles or 3 × 3 vectors	Cartesian positions stay fixed by default
Keep fractional positions	Scale atoms with the edited lattice
Periodic axes	Enable each axis separately

For a molecule without a source cell, the editor suggests a centred orthorhombic cell from its coordinate extent. Apply it explicitly to create a cell. Changes are local and reversible. Download current frame writes EXTXYZ with lattice and periodic-axis information.

Follow a trajectory

The timeline provides stepping, playback, scrubbing, and the current frame. Its menu holds playback settings, bookmarks, a reference frame, supplied scalar plots, displacement vectors, and supported pair-distribution analysis. Track displays the current atom positions and up to 50 previous frames.

Selections, pins, bookmarks, and references belong to the current workspace. Opening another dataset resets them; reloading the browser also clears them. Up to eight measurements, twelve bookmarks, and sixteen atom-image selections can be tracked at once.

Measurement and scalar plots follow the current frame. Pair-distribution and coordination plots aggregate frames; see trajectory analysis.

Search and shortcuts

Press Cmd/Ctrl+K or / to search. Type, use ↑ / ↓, then Enter. Settings results show their location, open the inspector, and highlight the control. Try atom color, edit lattice vectors, or transparent image.

Keys	Action
← / →	Previous / next frame
Shift+← / Shift+→	Back / forward ten frames
Space	Play / pause
R	Fit structure
1 / 2 / 3 / 4	3D / XY / XZ / YZ
E / V	Edit / View
C	Toggle cell
?	Full shortcut sheet and optional Vim navigation

For exports, see Figures and recipes.