Chemical Crystallography Oxford: Include And Exclude

The commands INCLUDE and EXCLUDE are very useful as they control which atoms are drawn at any one time. The syntax for both of the commands is very similar as they are effectively the reverse of each other.

EXCLUDE

These commands may be entered on their own and be follow by atom or element names. The syntax is :-

 nnCLUDE at1 at2 el1 el2

Once an atom has been EXCLUDED from the picture it is not drawn and it is not included in any calculations eg PACK or ENCLOSURE.

ALL The ALL sub-command is a 'blanket' command that applies the IN/EXCLUDE operation to ALL of the atoms in the current view. Therefore if we want to exclude more atoms than we want to include we can use EXCLUDE ALL to get rid of all of the atoms and then add in those we want by using INCLUDE.

GROUP The command DEFGROUP is available to define groups of atoms that are to be referred to as a whole. The IN/EXCLUDE command can be used with GROUP to remove or atoms all of the atoms in the group in the picture as required.

FRAGMENT The user can specify atoms to be IN/EXCLUDEd by defining groups of atoms as fragments. A fragment is defined by a single atom, and consists of all the atoms linked to it by the current CONNECTIVITY TABLE. That is, if atoms are excluded from the picture the bonds ARE NOT broken and FRAGMENT will use bonds involving excluded atoms in its calculations. The user can select this atom by typing or by clicking on it with the mouse. ie. EXCLUDE FRAGMENT C1 will exclude C1, any atoms joined to C1, any atoms joined to those atoms etc.

CELL It is often useful to see how the atoms being drawn relate to the unit cell. IN/EXCLUDE CELL is used to control the inclusion of the unit cell (in the LINE style) on the picture.

AREA Choosing INCLUDE or EXCLUDE AREA in the PC version allows the user to draw a polygonal area with the mouse. The polygon is created by clicking with the left button on the position required for the vertices. The polygon is closed by clicking close to the initial position. The mouse cursor is changed to a cross during polygon creation and to an arrow when you are close enough to the initial point for closure to occur. Hitting the <return> key or clicking with the right mouse button will abort the operation.

SELECT The select option is equivalent to EXCLUDE ALL followed by INCLUDE AREA. The polygonal area is chosen in the same way as described above and all atoms not within that area are excluded.

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10.1: Further related commands

For pictures with more than one 'type' of constituent atom three more commands will prove to be useful.

MASK

UNMASK

The MASK command has the same syntax as EXCLUDE ie.

 (UN)MASK at1 at2 el1 el2 ...

It is used to remove atoms from current INCLUDE operations - ie atoms that have been MASKed will not be included when using INCLUDE ALL. For example the user could MASK out solvent molecules from a diagram leaving the 'basic' asymmetric unit to be worked on. UNMASK can be used to re-include the required atoms. The sub commands ALL and GROUP are available for use with both MASK and UNMASK.

SWITCH

The SWITCH command causes any atoms that are EXCLUDEd from the picture to be INCLUDEd and vice versa. This command can be used in conjunction with MASK as any MASKed atoms WILL NOT be included in the picture after a SWITCH operation.

Consider an asymmetric unit containing an anion, a cation and some solvent. The user could MASK out the solvent atoms. EXCLUDE the anion and obtain pictures of the cation atoms. The SWITCH command then allows the user to examine the anion without having to INCLUDE and EXCLUDE atoms, and the solvent atoms remain excluded throughout.

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10.2: Generation of Dummy atoms

DUMMY

In certain circumstances it may be useful for the user to be able to generate new 'dummy' atoms from the initial atomic coordinates. One example of this is a compound that contains a cyclopentadienyl ring. The bonding in such a system can either be represented as five M - C bonds or as a single bond to the ring's centre. The syntax for the command is:

 INCLUDE DUMMY d

where d is the name of the created atom. This must then be followed by a sub-command which defines the atoms position.

COORDS This specifies the atoms coordinates in unit cell fractions. The syntax is:

 COORDS x y z

CENTROID Alternatively, the atoms position can be defined relative to others already in the molecule. At least TWO atoms must be entered to define new atoms position and it is placed at the CENTROID of their coordinates. The syntax is:

 CENTROID at1 at2 at3 ...

ALL A further sub-command is available so that the new atom is placed at the centroid of all of the atoms in the molecule. This will prove particulary useful when trying to alter the spacegroup of a structure eg to convert from P 1 to P -1 as the centre of inversion will lie at the newly generated dummy atom whose coordinates are output once they have been calculated.

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10.3: Example

To create a dummy atom in the centre of a cyclopentadienyl ring you would use:

 INCLUDE
 DUMMY d1
 CENTROID C1 C2 C3 C4 C5

Cameron Manual

Chapter 10: Include And Exclude

10.1: Further related commands

10.2: Generation of Dummy atoms

10.3: Example