Chemical Crystallography Oxford: Connectivity Control

It is important that the user has complete control over the bonds displayed in a drawing. The CONNECT group of options is a complicated one but has been designed so as to provide to user with a fully flexible set of commands.

CONNECT is used in one of two ways, either on its own or with a modifying sub-command.

CONNECT
The syntax for this command is:

 CONNECT X Y dmin dmax

This will create two lists of atoms (one from X and one from Y which may be atoms, elements or * as required) and uses these lists when calculating connectivity. dmin and dmax are in angstroms. The distances between all combinations of the atoms in the two lists are determined. If distances any lie within the specified dmin -> dmax range (and the bonds do not already exist) they will be added into the connectivity lists. To connect up CU1 O bonds for example you could use:

 CONNECT CU1 O 0.0 2.0

which would create one list - containing Cu1 only - and another list - containing all of the oxygen atoms - and then search for inter-list bonds. In this way, if any O - O bonds exist within the given range they will NOT be found. Note that if you require connections to be calculated between atoms of the same type you use:

CONNECT X X dmin dmax.

ALL CONNECT ALL requires two arguments dmin and dmax. The result is identical to CONNECT above except that ALL of the atoms are included in the calculation.

 CONNECT ALL 0.0 2.0

will draw all bonds that fall within the 0.0 - 2.0 angstrom range.

DEFAULT CONNECT DEFAULT requires no arguments. This command does two things:

 1)      Reset all of the connectivity radii
         to their initial values
 2)      Calculate the connectivity according
         to these radii.

It is effectively a 'start again' option as it removes any changes in bonding that have been introduced with the JOIN, REMOVE etc options.

RADII This is a sub-command of CONNECT and comes immediately after it. It requires the following arguments:

 CONNECT RADII X r

where X is the name of an atom or element and r is its new connectivity radius. The connectivity of this atom/element is then redetermined.

COVALENT

IONIC

VANDERWAALS These subcommands set the specified atoms to appropriate connectivity radii eg CONNECT RADII IONIC N. The further subcommand ALL can be used to set all atoms.

HBONDS This command enables the user to search for hydrogen bonds within the structure. The syntax is :-

 CONNECT HBONDS dmin dmax X Y

dmin/dmax is the range for searching (in angstroms), X/Y are atoms/elements to be included in the search. For a H-bond to be valid it must be bonded to one of the atoms in the list X,Y etc AND be within the range of another of the atoms. For example, if we are searching for H-bonds involving oxygen atoms:

 CONNECT HBONDS 0.0 2.5 O

will achieve this. There may well be eg C - H - O linkages within the range but only O - H - O ones will be registered. In this way we can filter the search and set a large value for dmax so that all the H-bonds are discovered without obtaining spurious information. The bond style used for H-bonds is dotted.

INTER

This option is intended to be used after a PACK or ENCLOSURE operation. This will find connections between atoms which have DIFFERENT packnumbers - ie. between assymetric units or between different GROUPS if PACK or ENCLOSURE GROUP has been used. The bonds are in the DOTTED style when generated. The syntax is:

 CONNECT INTER O C 0.0 3.0

as for CONNECT itself.

DOTTED

The CONNECT command can also be used if bonds already exist to alter the style. There are three options:

 CONNECT DOTTED at1 at2
 CONNECT DOTTED at1 el1
 CONNECT DOTTED el1 el2

These change the style of the single bond at1-at2, the style of any el1-at1 bonds and the style of any el1-el2 bonds respectively. Note that in the latter case, el1 and el2 may be the same element ie you can make all C-C bonds dotted.

JOIN

DOTTED

FULL

Another connectivity header command is JOIN. This is a more specific command which is used to make a new bond. The syntax is:

 JOIN DOTTED at1 at2
 JOIN FULL al1 at2

This will create a new bond between at1 and at2 of the specified type.

REMOVE
This is the reverse command to JOIN. It will break the bond between the specified atoms. The syntax is:

 REMOVE at1 at2

DISCONNECT

This command is the reverse of CONNECT.

 DISCONNECT C O 0.5 1.5

will get rid of any C-O bonds that are OUTSIDE the range 0.5 - 1.5 angstroms.

ALL DISCONNECT ALL removes all of the connectivity information.

GROUP DISCONNECT GROUP is intended primarily for use with disordered structures although other uses can be envisaged. For example a substituent may be 'flipping' between two sites generating very short distances between atoms in different groups. It is not possible to DISCONNECT these bonds since some of the distances may appear to be 'normal'. To get over this, each disordered part is defined as a group (See DEFGROUP) and DISCONNECT GROUP is used to remove any bonds that exist between them. The syntax is:

 DISCONNECT GROUP group1 group2

ATOM

This command deletes ALL bonds involving the specified atom. The syntax is:

 DISCONNECT ATOM at1

There are three other commands which either relate to connectivity or to how the bond is represented on the output device.

TAPER
This controls the bond tapering. It has an initial value of 2.0. Increasing this increases the tapering of the bonds. This tapering is useful as it introduces a 3-D effect into the drawing. If tapering is not required then entering:

 CONNECT TAPER 0.0

will achieve this.

THICKNESS

This command controls the thickness (radius) of the bonds in angstroms. It requires one argument, whose default value is 0.02.

 CONNECT THICKNESS 0.04

will double the radius of the bonds as drawn.

TOLERANCE

This sets the tolerance used when determining whether or not a bond exists. The formula used is:

 If  dist < ( C1 + C2 ) * tol  then a bond exists

where C1 and C2 are the connectivity radii of the atoms in question. The initial value of 'tol' is 1.1 ie the interatomic distance has to be no more than 10% greater than the sum of the two connectivity radii for a bond to be found. The syntax for the command is:

 CONNECT TOLERANCE n

Cameron Manual

Chapter 12: Connectivity Control

12.1: CONNECT

12.2: Miscellaneous CONNECT commands