Viewer guide

The interface is one continuous scientific workspace. The structure stays on the canvas while View, Edit, Analyze, and Export expose one task at a time. On narrow screens, Tools opens the same View/Edit/Analyze inspector as a bottom sheet; its arrow expands the sheet to full height.

Canvas

  • Drag to rotate.

  • Secondary-drag or middle-drag to pan.

  • Scroll or pinch to zoom.

  • Click an atom to select it.

  • Shift-click to extend or reduce the selection.

  • Shift-drag empty space for box selection.

  • Click empty space to clear the selection.

The small canvas controls fit the structure and select perspective, XY, XZ, or YZ views. Camera orientation and selection stay stable while frames change.

Edit

Choose Edit or press E for source-data changes. Cell + structure shows the formula, atom and frame counts, and boundary conditions. The cell editor accepts either lengths and angles or the full 3 × 3 lattice vectors. Each periodic axis can be enabled separately. By default, changing the cell keeps Cartesian atom positions fixed; enable Keep fractional positions when atoms should scale with the lattice.

Molecules without a source cell receive a centered orthorhombic suggestion based on their coordinate extent. Applying it creates a cell; nothing is added automatically.

Clicking an atom opens its read-only scientific details in Analyze. Choose Edit atom there, or choose Selected atom while Edit is open, to change element identity and Cartesian coordinates. Element changes apply to the whole structure, while coordinates apply to the displayed frame. Edits are local, reversible, and used by figure export. Download current frame writes the edited structure as EXTXYZ, including lattice and periodic-axis information.

Analyze

Analyze is always available. With no selection it explains the selection gestures. One selected atom shows its identity, position, charge, force, and velocity values without exposing accidental edits. Ordered selections of two, three, or four atoms show a distance, angle, or dihedral. Larger selections show their formula, centroid, extent, and unique-atom count.

The selection bar exposes actions that apply to the current selection:

  • Select expands the selection to an element, molecule, residue, connected component, or atoms within a distance.

  • Plot follows a distance, angle, or dihedral across the trajectory.

  • Pin keeps a measurement for recall or comparison.

  • Track shows the selected atoms’ recent paths.

  • Analyze opens pair-distribution setup for suitable periodic data.

  • Details inspects a single atom.

  • Summary reports formula, center, extent, and atom count for larger selections.

Periodic measurements use the exact minimum image by default. Switch to displayed images when measuring a chosen replica.

Saved selections and pinned measurements last for the current workspace and dataset. Reloading the browser clears them.

View

Choose View or press V to open the controls supported by the current source.

Representations are explicit: ball-and-stick, spacefill, licorice, lines, ribbon, coordination polyhedra, and surface. Atom and bond size, coloring, hydrogen visibility, and interactive quality are adjustable in the same inspector. Light and dark appearance are explicit View settings. PQViewer chooses a sensible initial display for the loaded data, but every representation and layer remains directly controllable; the inspector does not require a scientific-system preset.

Coordination geometry follows the visible bonding topology. Planar ligand shells are shown as polygons; non-planar shells are shown as polyhedra. When bonds are inferred, PQViewer uses the nearest distance shell so longer contacts do not inflate coordination. If several metal sites are available, transition metal coordination is preferred; this keeps perovskites focused on their octahedral network. Polyhedra that protrude outside a displayed single cell are omitted, and dense structures show a deterministic subset.

A single visible unit cell does not draw minimum-image bonds through its boundary. Repeated-cell views retain bonds between neighboring displayed cells.

Overlays

  • Show or hide water

  • Show or hide the periodic cell

  • Display force and velocity vectors with adjustable scale

Periodic

  • Atom coordinates: wrap each atom into the displayed cell

  • Molecule coordinates: keep known molecules whole while wrapping

  • Unwrapped coordinates: follow continuous motion across frames

  • Center the displayed cell at the PQ origin, structure, or selection

  • Mirror the display along a, b, or c

  • Repeat periodic images along each available axis

These controls change the display only. They do not rewrite source coordinates. Use command search for Source coordinates when the stored coordinates need to be shown without display wrapping.

The interactive view uses the locally bundled 3Dmol renderer. If it cannot initialize, PQViewer keeps the established Three renderer available as a fallback.

Export

Export opens one figure inspector for size, DPI, PNG or TIFF, white or transparent background, projection, labels, legend, scale bar, and reproducible figure recipes. The interactive 3Dmol canvas is not treated as publication output: figures use the independent high-quality renderer. Press Cmd/Ctrl+Shift+S for a quick 2400 × 1800 PNG with publication defaults.

Trajectory

The timeline appears for multi-frame data. It provides first, previous, play/pause, next, last, scrubbing, and the current frame. Its menu contains:

  • playback rate, stride, and once, loop, or rock mode

  • frame bookmarks

  • one reference frame

  • supplied scalar-property plots

  • displacement vectors after a reference frame is set

  • pair-distribution and coordination analysis when supported

Property and measurement plot cursors follow the displayed frame. Selecting a point in those plots navigates back to its frame. Pair-distribution and coordination plots aggregate frames and are not linked to one current frame.

Start selected-atom trails with Track in the selection bar or command search. Trails show the current position and up to 50 previous frames. The reference-frame menu controls displacement vectors.

Selections, pins, bookmarks, and references belong to the current workspace and reset when a new dataset is opened. Up to eight measurements, twelve bookmarks, and sixteen atom-image selections can be tracked at once.

Search and keyboard

The central Search control finds atoms, settings, and commands. Press ⌘K on macOS, Ctrl+K on Linux and Windows, or / on any platform. Type to filter, use ↑ and ↓ to move through results, and press Enter to open the selected setting or run the selected command. Setting results show their path, such as View › Layers › Bonds or Edit › Cell › Vectors, then open collapsed sections, scroll the setting into view, and highlight it briefly.

Natural scientific terms are indexed. Queries such as bond across cell, atom color, edit lattice vectors, distance, dark mode, and transparent image lead to the relevant control. Search also accepts commands such as select within 3 Å of selection.

Keys

Action

← / →

Previous or next frame

Shift + ← / →

Move ten frames

Home / End

First or last frame

Space

Play or pause

M

Bookmark the current frame

R

Fit the structure

1 / 2 / 3 / 4

Perspective / XY / XZ / YZ

↑ / ↓, Enter

Browse atoms and toggle selection

E / V

Edit / View tools

D

Light or dark appearance

B

Toggle lines and ball-and-stick

C / F / W

Toggle cell / forces / water

Cmd/Ctrl+O

Open files

Cmd/Ctrl+Shift+S

Export a figure

?

Shortcut sheet

Escape

Close the active surface or clear selection

Optional Vim navigation is enabled in the shortcut sheet:

Keys

Action

h / l

Previous / next frame

H / L

Back / forward ten frames

gg / G

First / last frame

:

Search atoms, settings, and commands

Ctrl+[

Close the active surface

Pointer controls remain available when Vim navigation is enabled.