Symmetry

There are many ways that symmetry can be important/useful/beautiful to look at in macromolecular structures. A typically application is the reconstruction of a symmetric oligomer from a few subunits. PyMOL has tools that can help with this type of analysis or depiction.

Expanding crystallographic symmetry

Structures determined by X-ray crystallography are typically deposited as files containing the coordinates for one asymmetric unit (ASU). Knowledge of the symmetry operators that describe how the ASUs are arranged relative to each other allows the arrangement of the crystal lattice to be recreated. PyMOL can read this symmetry information from the input coordinate file and recreate the neigbouring copies of the ASU using symmexp.

PyMOL's built in symmetry expansion functionality is available as A->generate->symmetry mates for an object or as the symexp command.

The SuperSym plugin has additional unit cell and symmetry axis tools.

Displaying symmetry axes

Often it is necessary to be able to find and draw symmetry axes. There are some contributed scripts that help do this including Symmetry Axis, for which you need to know the coordinates and direction of the axis you would like to draw, and RotationAxis, which does an excellent job of displaying symmetry relationships between selections.