phenix.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 phenix.explore_metric_symmetry is in the comparison of related unit cells, that are related by a linear recombination of their basis vectors.
A list of keywords and concise help can be obtained by typing:
phenix.explore_metric_symmetry
Output:
Usage: phenix.explore_metric_symmetry [options]
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 spacegroup
before higher metric symmetry is sought.
--graph=GRAPH A graphical representation of the graph will be
written out. Requiers 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 spacegroups is
given for the given specified unit cell and spacegroup combination. If a
second unit cell is given, linear combinations of the basis vector of one
unit cell are sought that match the other.
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.
Constructing a point group graph given some basic information:
phenix.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:
phenix.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