Editing structures#
Editing is enabled by Edit → Editing mode (Ctrl+E). Every operation can be undone (Ctrl+Z; redo with Ctrl+Shift+Z or Ctrl+Y), a supercell and a change of lattice parameters included, and both keep the edits made before them. Edit → Restore geometry (Ctrl+R) returns a structure to the state in which it was read.
Switching between the crystallographic and primitive settings is a way of looking at a crystal rather than a change to it, so on its own it is not an undo step. Edits are carried into the other cell, and then it is one. An edit to one atom of the primitive cell reaches every copy of it in the crystallographic cell. The other way, an edit that treats differently atoms the centring makes copies of (one of two centred chains turned) leaves no smaller primitive cell to show it in, and you are asked before it is dropped, which is undoable.
Selection#
An atom is selected by clicking it and added to the selection with Ctrl held down; clicking the background clears the selection. Edit → Select all (Ctrl+A), Clear selection and Invert selection act on the whole structure.
Moving atoms#
A selected atom is moved by dragging it; its periodic images move with it, and a selection of several atoms moves as a unit. The arrow keys displace the selection by a small step, and Edit → Translate selected… applies a given displacement.
Edit → Rotate selected… (also Rotate… in the Geometry panel) turns the selection about an axis. The axis can lie along a lattice vector of the cell on screen, along x, y or z, through two selected atoms (a bond, or the length of a chain), or along a typed direction; it passes through the centroid of the selection, one of its atoms, the origin or a typed point. The view follows the angle as it is changed, and nothing is applied until OK; the rotation is then a single undo step. Positive angles turn anticlockwise looking down the axis. Periodic images turn with their atoms, so a chain selected across a face of the cell turns as one piece and the crystal stays periodic.
To turn one chain of a polymer crystal about its own length, select the chain and rotate it along the chain’s lattice vector, through the centroid of the selection.
Adding and removing atoms#
Add atom in the Structure panel adds one atom of the element chosen beside it. It appears in the middle of the structure (the middle of the cell along each direction that repeats, and among the atoms along each direction that does not, so that a new atom on a slab or a polymer lands on it rather than out in the vacuum) and is selected, ready to be dragged or given exact coordinates.
Delete selected (Del)
Duplicate selected (Ctrl+D)
Set element of selected…, which opens a periodic table
The cell#
The Cell menu acts on the lattice rather than on the atoms:
Crystallographic cell and Primitive cell select which of the two is displayed.
Lattice parameters… edits a, b, c, α, β and γ of the cell on screen: the crystallographic cell when it is shown, the primitive one otherwise. The atoms keep their fractional coordinates, edits included, and the crystal keeps facing the way it did. Restore geometry returns to the cell that was read.
Supercell… expands the cell. Edits are carried into it. An edit made in one cell of a supercell only — an atom removed from one of them — is carried into a supercell that is a whole multiple of it; for any other size you are asked whether to start again from the structure as read.
Complete coordination at cell boundary draws what the cell holds with its coordination complete. A molecule is drawn whole wherever it touches the cell. A framework (silicon, rock salt) is drawn with the atoms on the faces, edges and corners of the cell, and with all the ligands of each cation in it (up to eight), so every Na of rock salt has its six Cl. A chain or a layer in a crystal (a polymer, brucite) is drawn as a framework is, and each of its coordination centres is given all its neighbours, so chains run one bond past each face and every cation keeps its full coordination. The atoms added are atoms of the structure like any other: counted, selectable, and moved by the phonon modes. This affects the drawing; the deck written for CRYSTAL contains the cell itself. Edits are kept when it is switched on or off.
Point symmetry analysis and Brillouin zone… are described in Symmetry and Band paths.
The Info panel is recomputed after each operation, so the space group shown is that of the current structure.
Measurements#
The Geometry panel is in three sections, Measure, Lattice planes and Atoms, each folded or unfolded with a click on its title. The ones left open stay open in every tab and the next time the program is started.
Measure measures the current selection:
Atoms selected |
Quantity |
|---|---|
1 |
the position of the atom |
2 |
a distance |
3 |
an angle |
4 |
a dihedral angle |
Measurements remain drawn in the view and can be coloured individually or by type. The Thickness slider sets how thick the lines of distances, angles and dihedrals are drawn, in Å: those selected in the list, all of them when none is selected, and the ones measured next. A plane through the selected atoms is fitted under Lattice planes.
Lattice planes#
A crystallographic plane is drawn from its Miller indices, with no atoms selected, in the Lattice planes section of the Geometry panel. The indices are quoted in the conventional cell. Hexagonal and trigonal crystals are written with four indices (h k i l), where i = −(h + k).
The plane is placed either at a position along its normal, in units of the interplanar spacing d(hkl), or through the selected atom. Position 0 is the plane through the origin, 1 and −1 its neighbours on either side. Negative positions are needed for planes with a negative index, such as (1 −1 0), whose family lies on that side of the origin.
Whole family draws every plane of the family across the cell, d(hkl) apart. Each is listed with its d(hkl) and the number of atoms lying on it, within 0.15 Å; Select the atoms on it selects those atoms, ready to be measured. The Opacity slider sets how see-through the selected planes are, or all of them when none is selected.
Fit to selected atoms goes the other way, from atoms to a plane. A fitted plane behaves like any other, but has no family.