Symmetry Options Dialog

This dialog lets you manually define symmetry operators and/or specify an offset between the spacegroup setting and the origin of your atomic coordinates.

Sometimes you may wish for more flexibility for defining symmetry: maybe you are using a non-conventional spacegroup setting (e.g., with its origin off-centred relative to CrystalMaker's "standard" setting), or you would like to enter symmetry generators (general equivalent positions, e.g., "1/2+x, 1/2-y, z") manually. The Symmetry Options dialog gives you this flexibility.

• You access the Symmetry Options dialog via the Edit Crystal dialog (if you're editing an existing crystal, select the Edit > Crystal... menu command; if you're starting off by defining a new crystal, select the File > New Crystal... menu command).
• In the Edit Crystal dialog, click the options button to display the Symmetry Options dialog.

Using a Spacegroup Symbol

You can choose to either enter a spacegroup symbol, or to enter your own general equivalent positions (GEP's).If you choose to type in the spacegroup yourself (by clicking the Use spacegroup tab), CrystalMaker will check your entry (you may see a warning triangle at the bottom of the dialog box). If you wish, you can examine any GEP'S that have been generated in this way by clicking the Show GEPs button.

• See Chapter 3: Building Crystals in the CrystalMaker-3 User's Guide for more information about spacegroup symbols and their representations.

Defining Symmetry Operators (GEPs) Manually

To enter general equivalent positions (GEP's) yourself, you need to click the Use GEPs tab. You should now specify the lattice type from the popup menu. Next you can enter GEP's in the editing fields. The GEP's should be of the form: "x y z", "1/2+x 1/2-y z", "-x -y -z", and so on. You can enter translations as fractions (e.g., 1/2) or decimals (0.5). Click the Add button to add your GEP to the list. You can also use the Copy, Edit, or Delete buttons when a specific row in the list is highlighted.

Origin Offset

When you type in a spacegroup symbol, CrystalMaker converts this to a set of general equivalent positions. In so doing, CrystalMaker is making an assumption about the absolute positions of your symmetry elements, relative to the unit cell's origin. There is a chance that this assumption is invalid: your symmetry elements may be offset relative to the CrystalMaker origin.

Most of the time you won't encounter problems, however there are two situations where problems may occur:-

1. Some crystal structures are published with their origins deliberately displaced from the "standard" setting given in the International Tables for Crystallography.
2. Certain, complex spacegroups can have more than one origin choice. The different choices are listed in the International Tables for Crystallography, and are also included in CrystalMaker's Spacegroups Assistant Dialog. (CrystalMaker's default origin choice almost always has centres-of-symmetry located at the unit cell origin. This choice may not always be the first-listed choice in the International Tables

In these circumstances, you need to tell CrystalMaker what the offset is. One way to do this is to enter an origin offset in the Symmetry Options dialog (you can enter the offsets as fractions, or as decimals); the offset is that required to map your existing coordinates onto CrystalMaker's unit cell. Alternatively, you can experiment with different origin settings listed in the Spacegroup Assistant dialog.

Origin Offset: Worked Example Spacegroup F d -3 m (number 227) has two origin choices:- Origin at the intersection of a screw tetrad axis (-4), a triad axis (3) and a mirror plane (m). Relative to this origin, there is a centre of symmetry with fractional coordinates (1/8, 1/8, 1/8). Origin at a centre of symmetry (-1). The translations required to move the origin (1) to origin (2) are: +1/8, +1/8, +1/8, parallel to x, y, and z-axes, respectively. (These are fractions of the unit cell edges a, b, and c.) CrystalMaker uses origin choice (2) - defined by centres of symmetry. So, if the atomic coordinates of a structure are described in terms of origin choice (1), they must be mapped onto CrystalMaker's origin by applying the translation: (1/8, 1/8, 1/8).

Where Next?

When you are satisfied with your symmetry settings, click the OK button to close the Symmetry Options dialog, and return to the Edit Crystal dialog. Note that the symmetry information is updated, with the origin offset displayed.

Main Menu

© 1999 CrystalMaker Software. All rights reserved