Root-mean-square deviation (RMSD) of two XYZ structures.

The root-mean-square deviation (RMSD) is calculated, using Kabsch algorithm (1976) for rotation, between two Cartesian coordinates (.xyz) or (.pdb) files.

For more information please read RMSD and Kabsch algoritm.

Usage

Type calculate_rmsd --help for all the arguments.

Pretty straight forward execution, clone and run as

calculate_rmsd molecule1.xyz molecule2.xyz

If it isn't then run it with Python 2.7

Citation

1. Kabsch algorithm: Kabsch W., 1976, A solution for the best rotation to relate two sets of vectors, Acta Crystallographica, A32:922-923, doi:10.1107/S0567739476001873

2. Quaternion algorithm: Michael W. Walker and Lejun Shao and Richard A. Volz, 1991, Estimating 3-D location parameters using dual number quaternions, CVGIP: Image Understanding, 54:358-367, doi:10.1016/1049-9660(91)90036-o

3. Calculate RMSD for two XYZ structures, GitHub, http://github.com/charnley/rmsd, doi: 10.5281/zenodo.46697

Note: some journals may require GitHub commit id.

Examples

Same structure, but translated in space, so the RMSD should be zero

calculate_rmsd examples/ethane.xyz examples/ethane_trans.xyz

You can also output (stdout) molecule1's coordinates centered and rotated to molecule2. Useful to visualize the difference. The output will be in XYZ format.

calculate_rmsd --output examples/ethane.xyz examples/ethane_trans.xyz

You can also use PDB format by using the argument -f pdb as seen:

calculate_rmsd -f pdb examples/1ypa.pdb examples/3ci2.pdb

Problems?

Make a issue or fork and fix it.

Credit and Copyright

Jimmy Charnley Kromann and Lars Andersen Bratholm