rmsd 1.2.2

Calculate RMSD using, translation and rotation, between molecules

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.

Installation

From PyPI

pip install rmsd

Download Python file

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

wget -O calculate_rmsd https://raw.githubusercontent.com/charnley/rmsd/master/calculate_rmsd.py

If you want to use it as a python package, then clone it the down and copy-paste the rmsd folder to the directory you need.

Usage

Type calculate_rmsd --help for all the arguments.

Pretty straight forward execution, clone and run as

calculate_rmsd molecule1.xyz molecule2.xyz

or

calculate_rmsd protein.pdb protein.pdb

Citation

• Kabsch algorithm:

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

• 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: http://dx.doi.org/10.1016/1049-9660(91)90036-o

• Implementation:

  Calculate RMSD for two XYZ structures, GitHub, http://github.com/charnley/rmsd, <commit hash or version number>

Please remmeber to cite this implementation when using it for scientific publications.

More usage examples

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

calculate_rmsd examples/ethane.xyz examples/ethane_translate.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_translate.xyz

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

calculate_rmsd -f pdb examples/ci2_1.pdb examples/ci2_2.pdb

Problems?

Submit issues on GitHub or submit pull requests.