Calculate an average structure.

The average structure has the average coordinates of the input models.

atomsAtomArrayStack or ndarray, dtype=float, shape=(m,n,3)

The structure models to be averaged. Alternatively, coordinates can be provided directly as ndarray.

averageAtomArray or ndarray, dtype=float, shape=(n,3)

Structure with averaged atom coordinates. If atoms is a ndarray and ndarray is also returned.

See also

rmsd, rmsf


The calculated average structure is not suitable for visualization or geometric calculations, since bond lengths and angles will deviate from meaningful values. This method is rather useful to provide a reference structure for calculation of e.g. the RMSD or RMSF.