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 trn code refers to cell translations where the code 555 refers to a displacement of 0,0,0 (e.g. the code 645 refers to a displacement of +1,-1,0).
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)).