Cameron Manual

Chapter 15: Symmetry Input

: 15.1: Input of symmetry operators; 15.2: Example of Space Group Input; 15.3: Other symmetry related operations

15.1: Input of symmetry operators

CAMERON is a crystallographically oriented program and hence many of its functions require the use of symmetry operators. There are two methods of inputting the symmetry operators, inputting the Spacegroup symbol and inputting the individual operators themselves.

SPACEGROUP

The SPACEGROUP command is followed by the symbol, which must contain all UPPER CASE letters. If the symbol is in a non-standard setting then the full symbol must be entered. For example P 21 will be interpreted as P 1 21 1 which is the standard setting, if P 21 1 1 is required then the "1's" must be entered to force the choice of unique axis.

The syntax of the command is :-

SPACEGROUP X X X X

where X are "fields" of the symbol, with spaces between fields ie entered as P 21 and NOT P21. The program will then output the operators that have been calculated for the symbol . Note that if a centre of inversion is present the inverted operators will NOT be shown. Also the operators generated from the centring vectors - eg 1/2 1/2 1/2 for body centring - will NOT be shown. The complete list of operators used for packing etc can be found by entering INFO SYMMETRY.

SYMMETRY

The input of symmetry operators can be done "by hand" if required. There are several steps and sub-commands available to do this.

OPERATORS

This sub-command MUST be entered even if only the x y z operator is to be included. The syntax is :-

SYMMETRY OPERATORS x y z -x y+1/2 -z ...

with the operators being entered with the translational part in fractional form ( 1/2 , 1/3 , 1/4 , 2/3 , 1/6 , 5/6 are recognised ) which must come after the x/y/z as required. The fractional part must be linked to the x/y/z part with a + or - sign. Note that NO spaces are allowed within each part of the operator. This is so that ambiguities cannot arise.

CENTRE

This command is used to introduce a centre of inversion into the symmetry information it must be followed by a centring letter (P,A,B,C,I,F,R) or the command VECTORS.

NOCENTRE

This command is used to specify that there is no centre of inversion - the centring vectors are the specified by letter or by using VECTORS.
VECTORS

This command enables the user to introduce centring vectors into the symmetry operators eg for body centring use :-

VECTORS 0 0 0 1/2 1/2 1/2

USE

NOUSE These commands allow the user to omit certain symmetry operators from the packing calculations. The command is followed by the operator numbers (found using INFO SYMMETRY) of the operators needed.
ALL This may be used to USE/NOUSE all of the operators. Note that using NOUSE ALL without following it with USE n will result in no atoms being generated after a pack operation!

15.2: Example of Space Group Input

In order to end up with the Spacegroup F m m m we require :-

SPACEGROUP F M M M

or

SYMMETRY OPERATORS
X Y Z  -X -Y Z  -X Y -Z  X -Y -Z
CENTRE
VECTORS
0 0 0
0 1/2 1/2
1/2 1/2 0
1/2 0 1/2

15.3: Other symmetry related operations

SETUNIT

This command causes the atoms that are to be included in the current picture to be set as the asymmetric unit. Their data then replaces that of the initially input atoms and they are used as the asymmetric unit from now on. This is useful if, for example only half of a molecule is present in the asymmetric unit. The other half can be generated with ADD and then SETUNIT is used to treat all of the atoms as the basic "building block". SETUNIT is a DANGEROUS command in that it cannot be undone - UNPACK will NOT reverse the operation. Therefore the user is prompted for confirmation before the command is executed. The syntax is simply SETUNIT.

ENANTIO
This command inverts the hand of the atoms in the asymmetric unit. Note that the operator applied is :-

-1  0  0
 0 -1  0
 0  0 -1

and no spacegroup changes that may be required are made.

SPECIAL

ON

OFF Controls the special position calculations that occur during packing to eliminate duplicate atoms. By default this is ON.