Chemical Crystallography

+ Frequently Asked Questions

+ Crystals Primer

+ Crystals User Guide

+ Crystals Manual

- Cameron Manual

1. Introduction

2. How To Get Started

3. Data Input

4. Outputting Data

5. Editing The Atom List

6. Obeying Files

7. Graphical Output Devices

8. View Direction Control

9. Include And Exclude

10. Drawing Style Control

11. Connectivity Control

12. Control Of Colour

13. Atom Labelling

14. Other Picture Controlling Commands

15. Symmetry Input

16. Crystal Packing Commands

17. Add And Move - Further Symmetry Related Commands

18. Distance And Angle Calculations

19. Information On Data Held Within The Program

20. Group Definitions

21. Miscellaneous Commands

22. How To Stop The Program

23. Menu Definition File

24. Some Useful Ideas

+ Index

Fri Jun 2 2000

Cameron Manual

Chapter 17: Add And Move - Further Symmetry Related Commands

17.1: ADD


17.3: MOVE

The PACK and ENCLOSURE commands already detailed allow the user to apply all of the symmetry operators in the spacegroup to the initial set of atoms in order to get a fully 'packed' result. In some cases however, the user may wish to apply only one symmetry operator or to apply ones that are not present in the spacegroup. The ADD and MOVE commands allow this.

17.1: ADD

The ADD command allows the user complete control over the symmetry operator used to generate new atoms. The first task of the user is to generate a list of those atoms to be used in the symmetry generation later. One of the following sub-commands is required :-
The names of atoms to be included in the pack list are specified here. Element names can also be used if required.
ALL refers to the atoms that are in the current list. If any atoms have been generated by previous PACK , ENCLOSURE or ADD commands then these will all go into the list.
ADD INITIAL means that the only atoms to go into the ADD list are those that were initially input.
This is followed by a group name. The group must have been previously been defined by the command DEFGROUP.

Once the ADD list has been created the user must then supply the symmetry operators which will act on the atoms in this list to generate the new atoms. The symmetry input is in two parts.
OPERATOR The symmetry operator may be input in decimal or fractional form eg

x y+1/2 z

-0.333-x -y -z

Decimal translations may come before or after the axis symbol. The fractions 1/2, 1/3, 1/4, 2/3, 1/6 and 5/6 are accepted by the program, but must appear after the x/y/z character. There must be spaces between the three parts but NO SPACES within the operator ie
X + 1/2 -Y  Z

will produce an error as it is not possible to tell whether you mean X+1/2, -Y, Z or X, +1/2-Y, Z. This strict input syntax is used to eliminate any ambiguities.
TRANS Translations can also be applied if required. The translations are applied in unit cell fractions. The syntax is :-
TRANS x y z



To generate an atom at x+1/2 y z from an atom at x y z we can use

or we could use
TRANS 0.5 0 0

The OPERATOR and TRANS commands can be used together if required. We can apply a symmetry operator followed by a translation. This reduces the errors that may occur when trying to combine the two things into one symmetry operator.
The use of INITIAL versus ALL is illustrated below. Start with :-
TRANS 1 0 0

which gives us a molecule at x y z and another at x+1 y z. Follow this with :-
TRANS 0 1 0

and we get four molecules, x y z , x+1 y z , x+1 y+1 z and x y+1 z. Following it with :-
TRANS 0 1 0

Gives us three molecules, x y z, x+1 y z and x y+1 z.

17.3: MOVE

The syntax for this command is identical to that for ADD. Therefore the commands available are :-



Which must be followed one (or both) of :-

The MOVE command applies a symmetry operator and/or a translation to all of the atoms held in the list defined by the ATOMS/ALL/GROUP/INITIAL commands. Unlike ADD therefore, the same number of atoms are present at the beginning and end of the operation.