BUNYIP
: Search for Additional Symmetry
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.