Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller
@article{Coutsias2005RotationalSA,
title={Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller},
author={Evangelos A. Coutsias and Chaok Seok and Ken A. Dill},
journal={Journal of Computational Chemistry},
year={2005},
volume={26}
}We clarify once again that Kabsch's method and the Quaternion method are mathematically equivalent methods, that is, that they contain identical information and, when properly understood and applied, lead to identical answers to any questions regarding least‐squares rotational superposition, either by proper rotations or by rotation‐reflections. We also provide the correct bounds for the eigenvalue spectrum. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1663–1665, 2005
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References
SHOWING 1-10 OF 16 REFERENCES
A comparison of three recently published methods for superimposing vector sets by pure rotation
- Chemistry
- 1989
Solutions to the rotational superposition problem published recently by Diamond [Acta Cryst. (1988), A44, 211-216] Kearsley [Acta Cryst. (1989), A45, 208-210] and MacKay [Acta Cryst. (1984), A40,…
A note on the rotational superposition problem
- Mathematics
- 1988
A rotation axis vector with magnitude tan (θ/2) for a rotation angle θ and a closely related unit vector of dimension 4 are used to show that : (i) the quadratic residual (weighted sum of squares of…
Superposition of molecular structures using quaternions
- Chemistry
- 1991
Abstract An algorithm is developed that finds the optimal orientation of a rigid molecular structure, represented by N reference sites, with respect to the same number of sites in an observed…
Using quaternions to calculate RMSD
- Computer ScienceJ. Comput. Chem.
- 2004
It is proved that the quaternion method is equivalent to the well‐known formula due to Kabsch, and an expression for the gradient of the RMSD as a function of model parameters is presented.
A generalized solution of the orthogonal procrustes problem
- Mathematics
- 1966
A solutionT of the least-squares problemAT=B +E, givenA andB so that trace (E′E)= minimum andT′T=I is presented. It is compared with a less general solution of the same problem which was given by…
Chirality in rotational superposition
- Mathematics
- 1990
It is shown that in the rotational superposition method proposed by Diamond (1988), which always produces orthogonal transformations with positive determinants, a simple test exists for the existence…
On the orthogonal transformation used for structural comparisons
- Mathematics
- 1989
Rotation matrices that minimize or maximize the sum of the squared distances between corresponding atoms for two structures are found using a constrained least-squares procedure solved analytically…
Matrix analysis
- Mathematics
- 1985
This new edition of the acclaimed text presents results of both classic and recent matrix analyses using canonical forms as a unifying theme, and demonstrates their importance in a variety of applications.
A solution for the best rotation to relate two sets of vectors
- Mathematics
- 1976
A simple procedure is derived which determines a best rotation of a given vector set into a second vector set by minimizing the weighted sum of squared deviations. The method is generalized for any…
A discussion of the solution for the best rotation to relate two sets of vectors
- Physics
- 1978
A method is discussed for obtaining the best proper rotation to relate two sets of vectors.