CRYSTALS
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Contents

+ 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. Archiving And Retrieving Views 8. Graphical Output Devices 9. View Direction Control 10. Include And Exclude 11. Drawing Style Control 12. Connectivity Control 13. Control Of Colour 14. Atom Labelling 15. Other Picture Controlling Commands 16. Symmetry Input 17. Crystal Packing Commands 18. Add And Move - Further Symmetry Related Commands 19. Distance And Angle Calculations 20. Information On Data Held Within The Program
21. Group Definitions
22. Miscellaneous Commands 23. How To Stop The Program 24. Menu Definition File 25. Some Useful Ideas 26. Cameron Manual
+ Menu and toolbar + Getting Started + Crystals Worked Examples + Index

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Wednesday 27 April 2011

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Cameron Manual

Chapter 21: Group Definitions

21.1: Example

For complicated structures it is sometimes useful to define GROUPS of atoms which can be referred to as a whole later. EXCLUDE, INCLUDE, COLOUR BONDS etc can all be used with the GROUP sub-command.

DEFGROUP

This is the main header command and is followed by the name of the group. Note that it is not possible to have group names that begin with GROUP itself - g1, g2 are valid names but group1, group2 are not. Up to twelve characters are allowed to define the group name.

ATOMS

This is followed by a list of atoms/elements to be included in the group.

GROUP

It is possible to have an atom as a member of up to three groups at once. You can therefore add groups into other groups (see Example).

FRAGMENT

The user can include atoms in a group by defining a fragment. The fragment definition requires a single atom. Any atoms joined to it, and any atoms to those etc are made part of the group.

DELETE

You can also remove atoms from groups if required.

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21.1: Example

Consider an molecule that contains a tri-phenyl phosphine. A use of the DEFGROUP command would be :- 

DEFGROUP PHENYL1
ATOMS C1 C2 C3 C4 C5 C6
DEFGROUP PHENYL2
ATOMS C11 C12 C13 C14 C15 C16
DEFGROUP PHENYL3
ATOMS C21 C22 C23 C24 C35 C36
DEFGROUP PPH3
ATOMS P
GROUP PHENYL1 PHENYL2 PHENYL3


If you then realise that there are two phosphorus atoms in the molecule P1 and P2 you can use :- 

DEFGROUP PPH3 DELETE P2


to remove P2 as it is not a member of the tri-phenyl phosphine group.


© Copyright Chemical Crystallography Laboratory, Oxford, 2011. Comments or queries to Richard Cooper - richard.cooper@chem.ox.ac.uk Telephone +44 1865 285019. This page last changed on Wednesday 27 April 2011.