Authors: James Hester and Syd Hall
Contact: Syd Hall, Crystallography Centre, University of Western Australia, Nedlands 6907, Australia
BUNYIP checks for consistent symmetry relationships within the model which are not described by the space group.
BUNYIP (Hester and Hall, 1996) scans the asymmetric set of atom coordinates and looks for the midpoints of any two sites that coincide with a centre (indicating the presence of an inversion), an axis (indicating a 2-fold rotation or screw) or a plane (indicating a mirror or a glide). If a large proportion of the possble midpoint combinations coincide with these symmetry elements within a specified tolerance, the coordinates of the centre, the equation of the line or plane is output along with the pairs of atoms that satisfy this requirement. In the case of the line or plane, additional data on the translation of the connected sites is listed. This provides information about a possible screw or glide translation parallel to the rotation axis or mirror plane.
For inversion centre:
The fractional coordinates x, y, z of the centre are output.
For rotation axis or screw:
The equation of the axis vector is
Ax + By + Cz
(e.g., the axis along c has C=1.0 and A=0.0, B=0.0)
For mirror plane or glide:
The equation of the vector normal to the plane is
Ax + By + Cz = D
(e.g., the mirror perpendicular to b has B=1.0; if the mirror is at y=1/4, then D=c/4 A)
The search is performed in Cartesian coordinates (orthogonal Angstroms) and no assumptions are made about the existing symmetry or cell, apart, that is, from aligning different molecules in the asynnetric unit into the optimally packed cluster. All coordinates are output in fractional units but the values of the deviations (all symmetries), translations (screws and glides) and the value of D (mirror plane equation) are in Angstroms.
Optimal clustering is an important aspect of the midpoint search, especially if molecular complexes of non-identical molecules are involved. It may be necessary in some cases to use the complx line to ensure that complexed molecules are "linked" identically. This may be required because the search for symmetry does not involve the application of known space group transformations, apart from in the preliminary clustering.