CrystalMaker Guide: Bonds Data Files

A type of output file summarizing atomic coordinates, bond distances and angles, for all sites in a structure.

You can look at the "bonds" file using any word-processor or text editor. The format of the bonds file can be summarised as:-

1. Summary of input data: Cell Parameters, symmetry, view direction
2. Listing of symmetry elements (General Equivalent Positions)
3. Fractional coordinates of atoms in the asymmetric unit
4. Fractional & orthogonal coordinates of all atoms in one complete unit cell
5. Listing of bonds, and bond-angles around each atom in the asymmetric unit.
6. List of bonded atoms

Summary of Input Data

The unit cell parameters, spacegroup symmetry, and view direction are listed. The general equivalent positions calculated from the spacegroup symbol, or from "SYMM" cards in the input file, are also listed.

Listing of Atomic Coordinates

Each atom is assigned a number ("num") and all atoms residing within a single unit cell are listed with their fractional and orthogonal coordinates, the latter being in Angstrom units.

Table of Bond Distances

For each atom in the asymmetric unit, a list of all atoms closer than 6.0 Å is given. The neighbouring atoms are identified by their element and site number, plus their number in the atoms list. Bond distances are given in Ångstrøm units.

Table of Bond Angles

For the sixteen nearest neighbours listed in the bond length table, a separate listing gives the various bond angles between different combinations of close neighbours.

Table of Bond Specifications

If bonds have been specifically requested (either through the Edit Bond Specifications dialog, or by BOND or BMAX cards in the input file), then a table of bonded atoms is given. On each line, a centrally-bonded atom is listed, with its atom number, followed by the atom numbers of its bonded neighbours. This is useful for identifying coordination numbers and polyhedra.

Previous | Main Menu | Next

© 1998 CrystalMaker Software. All rights reserved