**Authors:** Wolfgang Dreissig, Ruth Doherty, Jim Stewart & Syd
Hall

**Contact:** Syd Hall, Crystallography Centre,
University of Western Australia, Nedlands 6907, Australia

*BONDLA provides information about the geometric arrangement of the atoms in
the unit cell. This includes bond distances and angles, contact distances, and
dihedral angles. The search includes space group and adjacent cell symmetry.
The atoms are grouped in connected sets and the groups are optimally
clustered.*

BONDLA classifies interatomic distances as bonds or contacts or neither. This is determined by the distance relative to the sum of the radii of the atoms involved. The radii that are required for each atom type are:

Radii for each atom type are either read from the bdf, or supplied on
**atrad **lines (these supersede the values read from the bdf).
Default values are used for any atom types for which one or more of the radii
have not been specified. The classification of interatomic distances,**d***(A-B)*, is made as follows:

if | d < | rmin(A) + rmin(B) | ||

or | if | d > | rcon(A) + rcon(B) | not reported |

if | d >= | rmin(A) + rmin(B) | ||

and | if | d <= | rmax(A) + rmax(B) | considered a bond |

if | d > | rmax(A) + rmax(B) | ||

and | if | d <= | rcon(A) + rcon(B) | considered a contact |

All input atom sites are grouped for optimal connectivity and the connected
groups are clustered about the body centre of the cell, unless the user
specifies that the input sites should be used by entering the 'no-cluster'
option **nocl** on the **BONDLA** line. Note that the
clustered sites are *only* used for the *automatic* generation of
bond angles, distances, contact distances and dihedral angles (as specified by
the **bond** , **angle** , **cont** and
**dihe** options), *not* for the distances and angles
requested by **bond**, **angle**, **dihed**
and **nviron** lines. For these requests, the user has the option
of specifying the symmetry operation and the cell translation to be applied to
the input *coordinates*. Note that the **nviron** line
produces the distances to all atom sites within a specified maximum of the
entered atom site.

Control parameters and atom radii are listed first. Check these to ensure that
the distance and angle search has been correctly done. The coordinates of the
*input* atom sites are then listed. These will be followed by a list of
the coordinates of the 'clustered' atom sites, *only if *these are any
differences with the input coordinates. These will be followed by any symmetry
operations needed to form the connected sites or in the subsequent bond
distance searches.

The distances generated from the options **bond** and
**cont**, and the **nviron** line will be listed *in
the order of generation* unless the **sort** option is entered.
This option will cause these distances to be sorted *in order of ascending
magnitude*.

The option **dihe** will cause the dihedral angle involving all
possible connections to be produced. The number of dihedral angles can be large
even for modest structures. It may be preferable to use **dihed**
lines to request only the angles of interest. The dihedral angle table is not
redundant. If an entry appears for the bonded atoms A-B, a second entry will
not be given for the pair B-A. Dihedral angles about the pairs A-B will not be
included in the table if the coordinates of atom B bonded to atom A are not the
coordinates of atom B found for the connected set. This situation can arise
only if the connected set of atoms lies on a plane or centre of symmetry. In
these cases **dihed** lines may need to be used.

The space group symmetry and cell translation operations used to transform atom
sites are listed under the heading `sym trn`. These
`sym` numbers refer to the symmetry matrices shown and in the order of
input into the program * STARTX* (see the STARTX listing). The

Two types of data are output to the line file `pch`. The first is
the coordinates and standard deviations of the *connected* atom sites. The
second is the distance and angle data in a format suitable for publication
purposes. Note that brackets will be inserted into the atom labels if the
**brac** option is entered (e.g. the atom name `C23` is
listed as `C(23)`).