cctbx::sgtbx::lattice_symmetry Namespace Reference

Determination of lattice symmetry (Bravais type). More...


Classes

struct  reduced_cell_two_fold_info

Functions

double find_max_delta (uctbx::unit_cell const &reduced_cell, sgtbx::space_group const &space_group)
 Determines maximum Le Page (1982) delta of all two-fold axes.
space_group group (uctbx::unit_cell const &reduced_cell, double max_delta=3., bool enforce_max_delta_for_generated_two_folds=true)


Detailed Description

Determination of lattice symmetry (Bravais type).

Function Documentation

double cctbx::sgtbx::lattice_symmetry::find_max_delta ( uctbx::unit_cell const &  reduced_cell,
sgtbx::space_group const &  space_group 
)

Determines maximum Le Page (1982) delta of all two-fold axes.

See also: group()

space_group cctbx::sgtbx::lattice_symmetry::group ( uctbx::unit_cell const &  reduced_cell,
double  max_delta = 3.,
bool  enforce_max_delta_for_generated_two_folds = true 
)

References: http://www.ccp4.ac.uk/newsletters/newsletter44/articles/explore_metric_symmetry.html

From section "2.1. Determination of the lattice symmetry" in the CCP4 newsletter 44:

The determination of the lattice symmetry is based on ideas by Le Page (1982) and Lebedev et al. (2006). Given a reduced cell (e.g. Grosse-Kunstleve et al. 2004a), it is sufficient to search for two-fold axes to determine the full symmetry. Subjecting the two-folds to group multiplication produces the higher-order symmetry elements, if present.

Le Page (1982) searches for the two-folds by computing angles between certain vectors in direct space and reciprocal space. This search is relatively expensive. Recently Lebedev et al. (2006) introduced the idea of simply enumerating all 3x3 matrices with elements {-1,0,1} and determinant one. As an additional requirement group multiplication based on each matrix individually has to produce matrices exclusively with elements {-1,0,1}. There are only 480 matrices that conform to all requirements. Lebedev et al. (2006) argue that this set covers all possible symmetry operations for reduced cells. We were able to confirm this intuitive argument empirically via simple brute-force tests.

Only 81 of the 480 selected matrices correspond to two-folds. These are easily detected by establishing which of the matrices produce the identity matrix when multiplied with themselves (and are not the identity matrix to start out with). To replace the expensive search for two-folds in the original Le Page (1982) algorithm, the 81 two-fold matrices are tabulated along with the axis directions in direct space and reciprocal space. The axis direction in direct space is determined as described by Grosse-Kunstleve (1999). The axis direction in reciprocal space is determined with the same algorithm, but using the transpose of the matrix. The complete implementation of the algorithm for generating the table (essentially just six lines of Python code) can be found in the file cctbx/examples/reduced_cell_two_folds.py in the cctbx distributions.

The search for two-folds computes the Le Page (1982) delta for each of the 81 tabulated pairs of axis directions. The corresponding symmetry matrix for each pair is immediately available from the table. In contrast, the original Le Page algorithm requires the evaluation of 2391 pairs of axis directions, and the computation of the symmetry matrices involves expensive trigonometric functions (sin, cos) and change-of-basis calculations.

The matrices with a Le Page delta smaller than a given threshold are sorted, smallest delta first. Successive group multiplication as described in Grosse-Kunstleve et al. (2004b) and Sauter et al. (2006) yields the final highest lattice symmetry. The complete search algorithm is implemented in the file cctbx/sgtbx/lattice_symmetry.cpp.

Grosse-Kunstleve, R.W. (1999). Acta Cryst. A55, 383-395.

Grosse-Kunstleve, R.W., Sauter, N.K. & Adams, P.D. (2004a). Acta Cryst. A60, 1-6.

Grosse-Kunstleve, R.W., Sauter, N.K. & Adams, P.D. (2004b). Newsletter of the IUCr Commission on Crystallographic Computing 3, 22-31.

Y. Le Page The derivation of the axes of the conventional unit cell from the dimensions of the Buerger-reduced cell J. Appl. Cryst. (1982). 15, 255-259

Andrey A. Lebedev, Alexei A. Vagin & Garib N. Murshudov Acta Cryst. (2006). D62, 83-95. http://journals.iucr.org/d/issues/2006/01/00/ba5089/index.html Appendix A1. Algorithms used in the determination of twinning operators and their type of merohedry

Sauter, N.K., Grosse-Kunstleve, R.W. & Adams, P.D. (2006). J. Appl. Cryst. 39, 158-168.


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