Structure Viewer¶

Structure Viewer draws the structure of the selected crystal as a three-dimensional image using OpenGL.

Keyboard & mouse shortcuts¶

The window has a main 3-D view plus two small gizmos — the crystal-axes box (bottom-left) and the light-direction box (top-left) — and each responds to a left-drag differently. The main view uses ReciPro's standard OpenGL view navigation.

Shortcut	Action
`F1`	Open this page of the online manual
`CTRL`+`SHIFT`+`C`	Copy the rendered image to the clipboard
Left-drag the main view	Rotate the model
Left double-click an atom	Show its coordinates, nearest-neighbour distances, and bond angles
Right-drag up/down, or Mouse wheel	Zoom
Middle-drag	Pan
`CTRL` + Right-drag up/down	Change the camera distance (perspective mode only)
`CTRL` + Right double-click	Toggle orthographic / perspective projection
Left-drag the crystal-axes gizmo	Rotate the model (no in-plane spin)
Left-drag the light gizmo	Change the lighting direction

The application-wide CTRL+SHIFT shortcuts from the main window also work while this window is focused.

→ See 21. Keyboard & mouse shortcuts for every window at a glance.

Main area¶

3D crystal structure with light source, crystal axes, and atom legend.

The Size (W×H) box at the top right of the window sets the pixel size used when saving or copying the rendered image. The ProjWidth box next to it shows the width of the projected view in nm. Edit the value to zoom numerically — it stays synchronized with right-drag / wheel zooming on the view.

Save image, copy to clipboard (Ctrl+Shift+C), save movie (MP4).

Save movie opens the Movie setting dialog below. A movie can rotate the view, translate the projection center, or do both at once — tick Rotation and/or Translation:

Rotation: rotates the view at Speed (°/s; negative values reverse the direction) about the axis chosen below — Current projection (tilt direction picked with the arrow buttons), a Direction index [uvw], or the normal of a Lattice plane (hkl).
Translation: moves the projection center along the direction index [uvw] at Speed (lattice periods per second). This option appears only when the dialog is opened from the Structure Viewer, and while it is enabled Direction index is the only direction mode.

Set the movie length (Duration), the frame rate (FPS, 1–120), and the encoder quality (Quality, 1–100; higher values use a higher bitrate and give a larger file), choose the codec (H264 / H265), and press OK to generate an MP4 file. Include final frame appends one extra frame at t = Duration so the movie ends exactly at the final orientation/position. (The encode-speed list only labels the progress display and no longer affects the actual encoding.)

Bounds defined by cell¶

Specify the drawing range of the crystal. There are two modes, switched with the radio buttons at the top.

In this mode the a, b, c axes of the unit cell are the unit of the drawing range.

Center: central fractional coordinate of the drawing volume.
Range: upper/lower limit for each of the a, b, c axes.
Preset buttons on the right give frequently used values (e.g. 1×1×1 cell, 2×2×2 cell).

Bounds defined by crystal planes¶

In this mode the drawing area is bounded by a set of crystal planes. If the planes do not define a spatially closed region, ReciPro automatically falls back to a one-unit-cell bound.

Bound list¶

All bound planes registered for the current crystal. Use Add / Replace / Delete to manipulate the list; the leftmost checkbox temporarily disables a plane without deleting it.

To save the changes permanently, you must also press Add or Replace in the Main Window. Otherwise the changes are lost the next time you change the selection in the main crystal list.

H k l indices¶

Set the bound plane by its Miller index. The checkbox includes crystallographically equivalent planes generated from the selected (hkl).

Distance from origin¶

The distance from the centre of the crystal to the bound plane. The unit is selectable between d and Å. With d, the distance is the input value multiplied by the d-spacing of the selected (hkl). With Å, the value is the absolute distance. Changing one updates the other automatically.

Show bound planes / Opacity¶

Show or hide the bound planes themselves. When shown, Opacity sets transparency (0 = transparent, 1 = opaque).

Clip objects by bound planes¶

If checked, only the inside region defined by the bounds is rendered; atoms, bonds, and polyhedra that intersect the bounds are clipped.

Hide atoms¶

If checked, all atoms, bonds, and polyhedra are hidden — useful when only the cell or lattice planes need to be visualised.

Atoms¶

Coordinates, element, occupancy, radius, colour, material. Apply to same elements.

Atom list¶

The list of atoms in the crystal. Use Add / Replace / Delete to manipulate the list; the leftmost checkbox temporarily hides an atom.

To save changes permanently, click Add or Replace in the Main Window as well.

Element & Position¶

Label: free-text label for the atom (used in legends and tooltips).
Element: chemical element / ionisation state.
X, Y, Z: fractional coordinates. Real numbers in 0–1, or fractions such as 1/2 or 2/3.
Occ: occupancy, a real number 0–1.

Origin shift¶

Shifts every atom by the same fractional offset. Press a preset button (for example, to swap origin choice 1 / 2 for the same space group), or enter a custom (Δx, Δy, Δz) and press Apply custom shift.

Appearance¶

Per-atom radius, colour, and material.

Radius: drawn atomic radius.
Atom color: surface colour.
Material: texture / material properties used by the OpenGL shader.
Apply to same elements: applies the current radius and colour to every atom of the same element species.

Bonds & Polyhedra¶

Bond length thresholds, polyhedron display, edges.

Bond list¶

All bond/polyhedron rules registered for the crystal. Use Add / Replace / Delete; the leftmost checkbox temporarily disables an entry. As with atoms and bounds, Add / Replace in the Main Window is required to make the change permanent.

Bond property¶

Bonding Atom (center): element species used as the centre atom of the bond / polyhedron.
Bonding Atom (vertex): element species used as the vertex (the other end).
Length between … and …: lower and upper distance thresholds. Atom pairs outside this range are not drawn.
Bond Radius: drawn bond thickness (cylinder radius).
Alpha: bond transparency (0 = transparent, 1 = opaque).

Polyhedron property¶

Show Polyhedron: when checked, the polyhedron defined by the current bond is drawn (only if the centre/vertex set is geometrically valid).
Inner Bonds: show/hide the bonds inside the polyhedron.
Center Atom: show/hide the centre atom.
Vertex Atoms: show/hide the vertex atoms.
Color / Alpha: face colour and transparency.
Show Edges: draw the edges connecting the vertices.
Edge Color / Width: colour and line width of the edges.

Unit Cell¶

Translation, cell planes, edges.

Translation¶

Every space group has a default origin. To move the centre of the drawn unit cell away from that origin, set the translation along a, b, c.

Show cell plane¶

Whether to draw the six faces that bound the unit cell. When enabled, you can set the face colour and transparency.

Show edges¶

Whether to draw the unit-cell edges. The edge colour is configurable.

Lattice Planes¶

Miller index specification with crystallographic equivalents.

H k l indices¶

Specify the lattice plane by its Miller index. The checkbox optionally includes crystallographically equivalent planes generated from (hkl).

Translation¶

Translate the drawn lattice plane by an integer multiple of its d-spacing — useful for visualising successive planes of the same family.

Coordination¶

Coordination table and graph around the target atom.

Table (left side)¶

Lists which atoms surround the selected target atom and at what distance. The target atom is selected from the dropdown above the table.

Graph (right side)¶

Histogram of neighbour count versus distance, derived from the same data as the table. Adjust Bar Width until the bars cleanly separate the coordination shells — this gives a visual estimate of the coordination number.

Information¶

Rendering log (frame time, GPU info) and basic information about the selected atom. Under construction — fields may grow over time.

Projection¶

Projection mode (orthographic/perspective), depth fading, rendering quality, transparency mode.

Projection¶

Orthographic: perfect parallel projection (viewpoint at infinity).
Perspective: perspective projection from the viewpoint distance set by the slider.

Depth fading out¶

Fades distant objects in the depth direction. Objects farther than Far are fully transparent; objects closer than Near are fully opaque; intermediate objects interpolate linearly.

Projection center¶

Sets the centre of projection to the specified coordinates. Turn on Custom to enter arbitrary coordinates. Each coordinate is folded into the range −0.5 to +0.5 (one lattice period). A Translation movie (see the File menu) drives these values automatically.

Rendering quality¶

Drawing quality (mesh subdivision, anti-aliasing). Higher quality is slower — choose the setting that matches your GPU.

Transparency mode¶

Algorithm used for translucent atoms and polyhedra.

Approximate: fast but can be inaccurate when many translucent objects overlap.
Perfect: order-independent transparency — accurate but very slow, effectively requires a discrete GPU.

Symmetry Elements¶

The Symmetry Elements tab draws the space-group symmetry operators directly onto the 3D model (toggle with the Symmetry Elements toolbar button). Each class of element can be shown/hidden independently:

Rotation axes and screw axes
Mirror planes and glide planes
Inversion centres and rotoinversion axes

For each class you can adjust the symbol size, line width, and colour.

Misc.¶

Accessory controls: set the display sizes (light ball, axes, legend). Group by element toggles the legend display.
Bonded atoms: Show bonded atoms even if they are outside the boundaries keeps drawing atoms that are bonded to atoms inside the drawing range, even when they fall outside it.
Label: set the font size, colour, and other properties of the atom labels.

Button	Description
Axes	Show axis orientation (size = lattice constant)
Light	Set light direction
Legend	Atom legend
Atoms	Toggle atom objects
Labels	Toggle atom labels
Unit Cell	Toggle unit-cell edges
Sym. Elems.	Toggle the symmetry-element overlay (see above)
Reset Rotation	Return to the initial orientation
Like Vesta	Vesta-style appearance

Structure Viewer¶

Keyboard & mouse shortcuts¶

Main area¶

Menu bar¶

File menu¶

Tool menu¶

Tab menu¶

Bounds defined by cell¶

Bounds defined by crystal planes¶

Bound list¶

H k l indices¶

Distance from origin¶

Show bound planes / Opacity¶

Clip objects by bound planes¶

Hide atoms¶

Atoms¶

Atom list¶

Element & Position¶

Origin shift¶

Appearance¶

Bonds & Polyhedra¶

Bond list¶

Bond property¶

Polyhedron property¶

Unit Cell¶

Translation¶

Show cell plane¶

Show edges¶

Lattice Planes¶

H k l indices¶

Translation¶

Coordination¶

Table (left side)¶

Graph (right side)¶

Information¶

Projection¶

Projection¶

Depth fading out¶

Projection center¶

Rendering quality¶

Transparency mode¶

Symmetry Elements¶

Misc.¶

Toolbar¶

See also¶