a three-dimensional space. The generalization to dimensions is immediate. External links This SVD algorithm is described in more detail at http://cnx.org/content/m11608/latest/ A Matlab function is available at http://www.mathworks.com/matlabcentral/fileexchange/25746-kabsch-algorithm A C++ implementation (and unit test) using Eigen A Python script is available at https://github.com/charnley/rmsd. Another implementation can be found in SciPy. A free PyMol plugin easily implementing Kabsch is . (This previously linked to CEalign , but this uses the CE Algorithm. ) VMD uses the Kabsch algorithm for its alignment. The FoldX modeling toolsuite incorporates the Kabsch algorithm to measure RMSD between Wild Type and Mutated protein structures. See also Wahba's Problem Orthogonal Procrustes problem References With a correction in Bioinformatics algorithms