CrystalMaker Online Help

Edit Crystal Dialog

This dialog lets you create, or modify, crystal structures.

The Edit Crystal Dialog is the starting point for creating a new crystal structure - and you can also use it to edit an existing structure.

To create a new structure, select the File > New Crystal... menu command.
To edit an existing crystal structure, select the Edit > Crystal... menu command.

The dialog is divided into three major sections, corresonding to the main steps involved in defining a crystal: symmetry, lattice parameters, and the fractional coordinates of atoms in the asymmetric unit (this is the smallest part of a crystal's unit cell that, in combination with the symmetry, is sufficient to define the positions of all the atoms in a unit cell).

1. Symmetry

CrystalMaker requires information about the crystal symmetry, so that it can generate atoms in the unit cell. Usually one would input the crystal's spacegroup symbol here (a string of characters, e.g., "I 4.1/a c d", which represents the type, and arrangment of symmetry elements in the unit cell, and the lattice type).

There are three ways of specifying symmetry:-

by typing the spacegroup symbol in the spacegroup field (see Chapter 3: Building Crystals in the CrystalMaker User's Guide for a more detailed introduction to spacegroup symbols and their representation);
by using the Symmetry Assistant dialog (press the Assist button, then select your crystal system, lattice type, and finally spacegroup, from the popup menus);
by using the Symmetry Options dialog (press the Options button, then manually define your symmetry) this dialog is really designed for advanced users, but you may have to use it if your structural data are off-centered relative to the spacegroup settings used by CrystalMaker.

The spacegroup symbol is almost always given as part of a crystal structure refinement; if you do not have this information, you might want to try entering "P 1" in the spacegroup field: this tells CrystalMaker that your crystal has no symmetry, and the unit cell will only contain those atoms typed into the atomic coordinates list (see below).

2. Lattice Parameters

The lattice parameters define the size and shape of the unit cell. Six parameters are required: the edge lengths parallel to the crystallographic x, y, and z axes a, b, and c, respectively (these must be entered using Angstrom units, where 1A = 1.0E-10 m = 0.1 nm); and the three inter-axial angles, alpha (y ^ z), beta (x ^ z) and gamma (x ^ y).

The shape of the unit cell relates to the crystal symmetry, so in many cases you don't need to enter all six parameters. For example, if you've specified that your crystal is cubic, then only one parameter is required: the edge length, a (cubic symmetry implies that the unit cell has the shape of a cube, with all edge lengths the same, and all angles 90 degrees).

If you symmetry settings have been correctly understood by CrystalMaker, then you should find that some of the lattice parameter fields may vanish, to save you some typing. (Note for advanced users: you can override this setting using the Symmetry Options dialog - e.g., if you wish to display a high-symmetry crystal with a (symmetry-breaking) distorted unit cell.)

3. Atomic Coordinates

The fractional coordinates of all atoms in the asymmetry unit are given in the scrolling list.

Please note that the coordinates are fractions of the unit cell edge dimensions a, b, c (so for example, if an atom in a cubic crystal has orthogonal coordinates {2 A, 4 A, 6 A} and the unit cell parameter a (=b = c) is 10 A, then its fractional coordinates are {0.2, 0.4, 0.6}.

As explained earlier, this list doesn't necessarily represent all atoms in the unit cell; if you have specified some symmetry, then CrystalMaker will use your asymmetric unit as a basis for generating more atoms in the unit cell.

To display a list of all atoms in the unit cell, use the File > Export > Bond Data command. A text file will be produced summarizing all atoms in the unit cell and their local environments.

In addition to the fractional coordinates, you must supply the chemical element symbol (two characters, e.g., "Si") and a site label (maximum of six characters letters or numbers, but not spaces). (You can use the Info Window to display site labels next to selected sites or you can use the Label Atom tool to apply labels to individual atoms in the plot.)

Where Next?

When you've finished entering your crystal data, you can start defining interatomic bonding or atom colours, using the Bonds or Spheres buttons. To generate and display the crystal, click the Plot button.

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