Crystals User Guide

This instruction computes inter and intra atomic distances and angles. All necessary symmetry operators are automatically applied to ensure that values within the specified limits are generated. The user should check that there are no inexplicably short inter molecular contacts, as well as checking the ususal bond lengths and angles. The program will also compute e.s.d.s from the full covarience matrix (including symmetry effects). The information for this is taken from the least squares matrix, and the program will not permit this information to be applied to any other LIST 5 than that produced be the corresponding round refinement. It is thus fairly important to give your atoms systematic names and serial numbers, and to get the list into a convenient order AS SOON AS POSSIBLE. Even just changing the serial of an atom will inhibit the linking of the LIST 5 and the matrix.

This procedure computes the principal axes of inertia of a group of atoms. If they have unit weights or weights derived from their standard deviations, then the shortest axis is parallel to the normal to the best plane, and the longest is parallel to the best line.

This procedure computes the torsion angles for the specified atoms. e.s.d.s are not currently computed.

This procedure compares the current values of parameters with those requested in the restraint definitions. Current values differing significantly from those required should be carefully reappraised, since they indicate a conflict between the diffraction data and the hypotheses.

The six components of the anisotropic temperature factor can be transformed to define a three dimensional ellipsoid representing the harmonic motion of the atom. If free refinement of the U's leads to an ellipsoid with a negative volume, then the transformation becomes meaningless, usually indicating that there are grave deficiencies in the model or the data. For data collected at very low temperatures, the volume may go marginally negative, and restraints on the U's should stabilise the situation. The procedure AXES is called automatically after every round of refinement, to give warning of non-positive definite U's. Refinement will however continue even if some atoms are unsatisfactory. The result is generally a rapidly diverging process with rapidly increasing R factors.

This procedure tries to fit the atomic temperature factors to a rigid body composite temperature factor. This is partitioned into three parts, T representing the rectilinear vibration of the body, L representing its torsional libration, and S representing the coordination between these two parts. There are 20 independant terms to be evaluated in TLS for an unsymmetrical fragment not lying on a symmetry operator, so that a rigid body of this sort cannot be defined for less than 4 atoms. For a body of six atoms, the calculation might just be meaningfull, though there are problems with the conditioning of the matrix if the atoms lie close to a conic section. Under these conditions the maths cannot distinguish two correlated motions in T space from a corresponding libration in L space. The user should be aware that good agreement between U(obs) and U(calc) does not mean that the values of T, L and S have any physical significance.