Identifying symmetry in a map with map_symmetry



The routine map_symmetry will identify the symmetry in a map and create a file with the symmetry operations.


How map_symmetry works:

Map-symmetry uses the density at a set of randomly-chosen points in a map to identify the symmetry in a map from a set of pre-defined symmetry types that include point-group symmetry as well as helical symmetry. For each possible symmetry, the correlation of values at symmetry-related points is calculated. The score for the symmetry type is the square root of the number of elements in the symmetry multiplied by the map correlation for that symmetry.

By default, map-symmetry assumes that the principal axes of symmetry in a map are along x, y, or z, and that helical symmetry is helical along z. The software has a database of 45 common symmetry elements and point groups, along with alternative settings of some of these. The user can specify a specific symmetry type to examine (e.g., I for icosahedral or D7 for a 7-fold axis along z perpendicular to a 2-fold axis along x or along y), or all elements in the database can be examined.

You can also use map-symmetry to find general (point-group or non-point-group) symmetry using the keyword "find_ncs_directly=True". In this case a density search will be carried out using spheres of density in the regions where the map varies the most as templates. Any similar density (with any translations or rotations) will indicate map symmetry.

For helical symmetry, a Fourier transform of the density is examined along the c* axis to find periodicity along z likely to correspond to the helical translation. These likely translations (and integer fractions of them) are tested along with possible rotations to check for helical symmetry.


Standard run of map_symmetry:

Running map_symmetry is easy. From the command-line you can type:

phenix.map_symmetry symmetry=D7

where is a map (CCP4, mrc or other related format), and in this case you are specifying that only D7 symmetry should be considered.

Possible Problems

Specific limitations and problems:

Helical symmetry is assumed to be along the z-axis.


Additional information

List of all available keywords