Map Symmetry (cryo-EM)

Why

Some molecules, such as viruses, have high internal symmetry so you can reduce the cryo-EM map to the repeating unit. This can decrease the required computational resources and enable better averaging for improved signal to noise.

How

The phenix.map_symmetry program uses the density at a set of randomly-chosen points in a cryo-EM map to identify symmetries, which are selected from a set of pre-defined symmetry types (e.g., point-group symmetry and helical symmetry). The tool then creates a file with the symmetry operations.

By default, phenix.map_symmetry assumes the principle axes of symmetry in a map are along x, y, and z and that the helical symmetry is along z. The user can specify a specific symmetry type or look for all elements in the database of 45 common symmetry elements and point groups.

How to use the phenix.map_symmetry: Click here

Common issues

None.

Related programs and Documentation

• phenix.map_box: This program cuts out a box around selected atoms from a larger map. It can be used to extract the unique part of the map (using the extract-unique option).
• phenix.combine_focused_maps: This program creates a weighted composite map from a set of locally focused maps and associated models, where each part of each map is weighted by its correlation with the corresponding model.