- Cameron Manual

: 1. Introduction; 2. How To Get Started; 3. Data Input; 4. Outputting Data; 5. Editing The Atom List; 6. Obeying Files; 7. Graphical Output Devices; 8. View Direction Control; 9. Include And Exclude; 10. Drawing Style Control; 11. Connectivity Control; 12. Control Of Colour; 13. Atom Labelling; 14. Other Picture Controlling Commands; 15. Symmetry Input; 16. Crystal Packing Commands; 17. Add And Move - Further Symmetry Related Commands; 18. Distance And Angle Calculations; 19. Information On Data Held Within The Program; 20. Group Definitions; 21. Miscellaneous Commands; 22. How To Stop The Program; 23. Menu Definition File; 24. Some Useful Ideas

Fri Jun 2 2000

Cameron Manual

Chapter 16: Crystal Packing Commands

: 16.1: PACK; 16.2: Dealing with connectivity; 16.3: EXAMPLES; 16.4: ENCLOSURE; 16.5: Choice of enclosure "origin"; 16.6: Type of volume to be used; 16.7: EXAMPLE; 16.8: PACKING MORE COMPLICATED STRUCTURES; 16.9: UNPACK

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.

16.1: PACK

The PACK command allows the user to define a volume to be filled relative to the unit cell. One of two-sub commands is required to define this volume.

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:-

CUT CUT will generate all the atoms that lie within the defined volume. ie. the generation is "cut" at the boundary.

COMPLETE COMPLETE is most useful for molecular crystallographers. It will generate all the asymmetric units that have ANY ATOMS lying with the defined volume.

CENTROID CENTROID is similar to COMPLETE except that it calculates the centroid of the asymmetric unit (as though all of the atoms have equal weight) and includes only those which have their centroid within the defined volume. This is particulary useful for molecular crystallographers as it creates a picture without the "odd atoms" at the edge of the unit cell.

16.2: Dealing with connectivity

There are three other qualifying commands that apply to PACK :-

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.

16.3: EXAMPLES

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

Or alternatively,

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

16.4: ENCLOSURE

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.

16.5: Choice of enclosure "origin"

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.

16.6: Type of volume to be used

There are three different ways of defining the volume of enclosure:-

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.

CUT

COMPLETE

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.
INTRA
INTER
KEEP These sub commands have an identical meaning to those described for PACK above.

16.7: EXAMPLE

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

16.8: PACKING MORE COMPLICATED STRUCTURES

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 command GROUP.

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.

16.9: UNPACK

This command causes all atoms generated via PACK or ENCLOSURE to be removed from the calculations, drawings etc. It has no sub-commands. It also works with ADD and MOVE generated data.