Chapter 16: Crystal Packing Commands
There are two methods of crystal packing available, PACK and ENCLOSURE. Both use ALL of the symmetry operators in the Spacegroup to generate all of the atoms that lie within a user-defined volume. The commands ADD and MOVE are available if single symmetry operators are required. The difference between the two commands lies in the method of volume definition.
The PACK command allows the user to define a volume to be
relative to the unit cell. One of two-sub commands is required
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
If this command is omitted then the option chosen in the last
command will be used. If this is the first time PACK is used then
the default option.
Three sub-commands are available:-
There are three other qualifying commands that apply to PACK
This qualifiers means that the connectivity will be calculated
each newly generated asymmetric unit only. Any changes to the
eg with JOIN , REMOVE , CONNECT , COLOUR BONDS - will be undone.
the fastest option.
In this case connectivity is calculated once all of the atoms
been generated - therefore if any intra-unit bonds exist they
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.
Therefore, to create a picture containing all of the complete molecules within a cube of side equal to 2 unit cells we need :-
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
The enclosure command is more flexible than PACK as it enables the user to choose the "origin" for the atom generation. The first task is to specify this origin which is either a point in the unit cell or an 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
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.
There are three different ways of defining the volume of
Where r is the radius in angstroms of the sphere.
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
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.
CENTROID As with PACK a further sub-command can be used if desired to define the type of boundary handling used. CUT, COMPLETE and CENTROID have the same meanings as described above for PACK.
KEEP These sub commands have an identical meaning to those described for PACK above.
To generate all the atoms that lie within a sphere of radius 5.0 angstroms about a CU1 atom we use :-
ENCLOSURE ATOM CU1 SPHERE 5.0 CUT
To generate all the asymmetric units that have any atoms within a box of side 0.5 units around the unit cell centre we use:-
ENCLOSURE POINT 0.5 0.5 0.5 ANORTHIC 0.25 0.25 0.25 0.25 0.25 0.25 COMPLETE
And to generate all the atoms that lie inside a box centred on the point 0.25 0.25 0.25 and of sides x=1.0 y=2.0 and z=3.0 angstroms :-
ENCLOSURE POINT 0.25 0.25 0.25 ORTHOGONAL 0.5 0.5 1.0 1.0 1.5 1.5 CUT
The PACK and ENCLOSURE commands always work on the initial data-
unless a SETUNIT command has been issued. In some cases however, it is
more useful for the user to be able to deal with certain sections of the
structure separately. This is most likely to occur where there is more
than one distinct unit in the asymmetric unit. This is dealt with by the
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 *
This command causes all atoms generated via PACK or ENCLOSURE
removed from the calculations, drawings etc. It has no
It also works with ADD and MOVE generated data.