Cameron Manual

CELL
PACK CELL will cause the program to generate all the atoms that lie within the unit cell. This is the default option if no range for packing is input.

WINDOW
PACK WINDOW allows the user to define the volume in terms of the unit cell axes. It is followed by three pairs of numbers.

 PACK WINDOW xmin xmax ymin ymax zmin zmax
 

The values of xmin etc are relative to the unit cell origin. Therefore to define a volume of which contained all of the x axis, all of the y axis and the first half of the z axis we would use:

 PACK WINDOW 0.0 1.0 0.0 1.0 0.0 0.5
 

If more than one unit cell is required negative numbers and numbers exceeding one may be used.

One more sub-command may be entered after the WINDOW or CELL commands. If this command is omitted then the option chosen in the last PACK command will be used. If this is the first time PACK is used then CUT is the default option. Three sub-commands are available:

INTRA

INTER

KEEP
These deal with the treatment of connectivity calculations once the PACK has been carried out.

INTRA

This qualifiers means that the connectivity will be calculated within each newly generated asymmetric unit only. Any changes to the bonding - eg with JOIN, REMOVE, CONNECT, COLOUR BONDS - will be undone. This is the fastest option.

INTER

In this case connectivity is calculated once all of the atoms have been generated - therefore if any intra-unit bonds exist they will be found.

KEEP

This is the default option. Connectivity is copied from the unit used to do the packing - this includes colour and style changes if any - into the bond info of the new atoms. This is done for each asymmetric unit as it is generated and is slower than INTRA as it requires more comparisons to be carried out.

 PACK
 WINDOW 0.0 2.0 0.0 2.0 0.0 2.0
 COMPLETE
 

 PACK
 WINDOW -1.0 1.0 -1.0 1.0 -1.0 1.0
 COMPLETE
 

ATOM

If we wish to generate the atoms around Cu1 in order to examine the coordination environment for example we can use:

 ENCLOSURE ATOM CU1
 

POINT

Alternatively we can choose the centre of the unit cell:

 ENCLOSURE POINT 0.5 0.5 0.5
 

The POINT sub-command can be used if an atom does not lie at the point in question eg if we are examining a "hole" within a structure.

SPHERE
This will generate a sphere of enclosure about the origin. The syntax is:

 SPHERE r
 

where r is the radius in angstroms of the sphere.

ANORTHIC
This is used to generate an ANORTHIC box ie a box whose sides are parallel to the unit cell axes. As this box is directly related to the unit cell its dimensions are given in fractional coordinates. The syntax is:

 ANORTHIC -x +x -y +y -z +z
 

Therefore, to generate an anorthic box with sides extending one quarter of a unit cell in all six directions from the defined origin we use:

 ANORTHIC 0.25 0.25 0.25 0.25 0.25 0.25
 

ORTHOGONAL
This is used to generate a box whose sides are perpendicular to each other. The z axis lies along the current view direction and the x and y axes lie across and vertically up the screen respectively. The dimensions of this box is defined in a similar way to the ANORTHIC box except that they are given in angstroms. For example, to generate a box that is 4.0 angstroms wide in x, 1 in y and 0.5 in z we would use:

 ORTHOGONAL 2.0 2.0 1.0 1.0 0.25 0.25
 

It is important to note that this volume is related to the CURRENT view direction. The VIEW ALONG AXIS command can be used to orient the picture prior to carrying out this command if required.

 ENCLOSURE
 ATOM CU1
 SPHERE 5.0
 CUT
 

 ENCLOSURE
 POINT 0.5 0.5 0.5
 ANORTHIC 0.25 0.25 0.25 0.25 0.25 0.25
 COMPLETE
 

 ENCLOSURE
 POINT 0.25 0.25 0.25
 ORTHOGONAL 0.5 0.5 1.0 1.0 1.5 1.5
 CUT
 

GROUP

GROUP can be used directly after both PACK and ENCLOSURE. The syntax is:-

 PACK GROUP groupname CELL ...
 or
 PACK GROUP groupname WINDOW ...
 etc
 

This causes the groups to be packed individually, the CENTROID, COMPLETE and CUT commands are applied to the group and not to the asymmetric unit as a whole. Packs are cumulative, unless a PACK/ENCLOSURE is done without the GROUP sub command in which case the previously generated atoms are overwritten. Groups are defined with the command DEFGROUP.

If required, more than one groupname can be packed at once - they are all treated separately. All groups can be packed in turn if PACK GROUP * is used.