Chemical Crystallography Oxford: Group Definitions

Chapter 21: Group Definitions

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

Cameron Manual

Chapter 21: Group Definitions

21.1: Example