Purpose

iotbx.explore_metric_symmetry is a program that allows a user to quickly determine the symmetry of the lattice, given a unit cell, and determine relations between various possible point groups.

Another use of iotbx.explore_metric_symmetry is in the comparison of related unit cells, that are related by a linear recombination of their basis vectors.

Keywords

A list of keywords and concise help can be obtained by typing: iotbx.explore_metric_symmetry

options:
  -h, --help            show this help message and exit
  --unit_cell=10,10,20,90,90,120|FILENAME
                        External unit cell parameters
  --space_group=P212121|FILENAME
                        External space group symbol
  --symmetry=FILENAME   External file with symmetry information
  --max_delta=FLOAT     Maximum delta/obliquity used in determining the
                        lattice symmetry, using a modified Le-Page algorithm.
                        Default is 5.0 degrees
  --start_from_p1       Reduce to Niggli cell and forget the input space group
                        before higher metric symmetry is sought.
  --graph=GRAPH         A graphical representation of the graph will be
                        written out. Requires Graphviz to be installed and in
                        path.
  --centring_type=CENTRING_TYPE
                        Centring type, choose from P,A,B,C,I,R,F
  --other_unit_cell=10,20,30,90,103.7,90
                        Other unit cell, for unit cell comparison
  --other_space_group=OTHER_SPACE_GROUP
                        space group for other_unit_cell, for unit cell
                        comparison
  --other_centring_type=OTHER_CENTRING_TYPE
                        Centring type, choose from P,A,B,C,I,R,F
  --no_point_group_graph
                        Do not carry out the construction of a point group
                        graph.
  --relative_length_tolerance=FLOAT
                        Tolerance for unit cell lengths to be considered
                        equal-ish.
  --absolute_angle_tolerance=FLOAT
                        Angular tolerance in unit cell comparison
  --max_order=INT       Maximum volume change for target cell

Explore Metric Symmetry. A list of possible unit cells and space groups
is given for the given specified unit cell and space group combination.

The keywords unit_cell, space_group (or centring_type) define the crystal symmetry for which a point group graph is constructed.

The keyword max_delta sets the tolerance used the in determination of the lattice symmetry.

the keyword start_from_p1 in combination with the space group is equivalent to specification of the centring_type only.

If graphviz is installed, an a png file with the point group graph can be constructed by specifying the filename of the png graph with the keyword graph.

If a second crystal is specified by the keywords other_unit_cell, other_space_group (or other_centring_type) the unit cells will be compared. Using linear combinations of the smallest unit cell, possible matches for the large unit cell are sought. If desired, the larger unit cell can be expanded as well using the keyword max_order.

The tolerances in the unit cell comparison can be changed form their defaults (10% on the lengths and 20 degrees on the angles) using the keywords relative_length_tolerance and absolute_angle_tolerance.

Construction of a point group graph can be skipped using the key no_point_group_graph.

Examples

Constructing a point group graph given some basic information:

iotbx.explore_metric_symmetry --unit_cell="20,30,40,90,90,90" \
  --centring_type=P

All point groups between P 1 and P 2 2 2 will be listed

Comparing two related unit cells can be done using:

iotbx.explore_metric_symmetry --unit_cell="20,30,40,90,90,90" \
  --centring_type=P --other_unit_cell="40,80,60,90,90,90" \
  --other_centring_type=F