Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format
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larsbratholm Merge pull request #34 from charnley/dependency_fix
moved __version__ to setup file
Latest commit 53e0084 May 22, 2018


Calculate Root-mean-square deviation (RMSD) of Two Molecules Using Rotation

The root-mean-square deviation (RMSD) is calculated, using Kabsch algorithm (1976) or Quaternion algorithm (1991) for rotation, between two Cartesian coordinates in either .xyz or .pdb format, resulting in the minimal RMSD.

For more information please read RMSD and Kabsch algorithm.


You have molecule A and B and want to calculate the structural difference between those two. If you just calculate the RMSD straight-forward you might get a too big of a value as seen below. You would need to first recenter the two molecules and then rotate them unto each other to get the true minimal RMSD. This is what this script does.

No Changes Re-centered Rotated
begin translate rotate
RMSD 2.50 RMSD 1.07 RMSD 0.25


You can get the package via pip under the name rmsd,

pip install rmsd

or download the project from GitHub via

git clone

There is only one Python file, so you can also download that and put it in your bin folder.

wget -O calculate_rmsd
chmod +x calculate_rmsd


Type calculate_rmsd --help for all the arguments. Usage is pretty straight forward, call calculate_rmsd with two structures in either .xyz or .pdb. In this example Ethane has the exact same structure, but is translated in space, so the RMSD should be zero.

calculate_rmsd examples/ examples/

It is also possible to ignore all Hydrogens (useful for larger molecules where Hydrogens move around indistinguishable) and output the rotated structure for visual comparison. The output will be in XYZ format.

calculate_rmsd --no-hydrogen --output examples/ examples/

It is also possible to use RMSD as a library in other scripts:

import rmsd
import numpy as np
P = np.array([[-0.9835 ,  1.8109 , -0.0314 ],
       [ 0.1268 ,  1.8041 , -0.03242],
       [-1.4899 ,  3.2274 ,  0.18102],
       [-1.3504 ,  1.1535 ,  0.78475]])

Q = np.array([[-2.1217 ,  4.0933 ,  0.12713],
       [-1.0113 ,  4.0865 ,  0.12611],
       [-2.628  ,  5.5097 ,  0.33955],
       [-2.4885 ,  3.4358 ,  0.94328]])
print "RMSD before translation: ", rmsd.kabsch_rmsd(P, Q)
P -= rmsd.centroid(P)
Q -= rmsd.centroid(Q)
print "RMSD after translation: ", rmsd.kabsch_rmsd(P, Q)


Please cite this project when using it for scientific publications.


Submit issues or pull requests on GitHub.