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Cameron Manual
Chapter 16: Symmetry Input
- 16.1: Input of symmetry operators
- 16.2: Example of Space Group Input
- 16.3: Other symmetry related operations
- 16.2: Example of Space Group Input
[Top] [Index] Manuals generated on Wednesday 8 November 2006
16.1: 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.
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.
The input of symmetry operators can be done "by hand" if required. There are several steps and sub-commands available to do this.
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.
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.
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.
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
[Top] [Index] Manuals generated on Wednesday 8 November 2006
16.2: 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
[Top] [Index] Manuals generated on Wednesday 8 November 2006
16.3: Other symmetry related operations
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.
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.
[Introduction | How To Get Started | Data Input | Outputting Data | Editing The Atom List | Obeying Files | Archiving And Retrieving Views | Graphical Output Devices | View Direction Control | Include And Exclude | Drawing Style Control | Connectivity Control | Control Of Colour | Atom Labelling | Other Picture Controlling Commands | Symmetry Input | Crystal Packing Commands | Add And Move - Further Symmetry Related Commands | Distance And Angle Calculations | Information On Data Held Within The Program | Group Definitions | Miscellaneous Commands | How To Stop The Program | Menu Definition File | Some Useful Ideas ]
