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