Alignments and RMS fitting

The MDAnalysis.analysis.align and MDAnalysis.analysis.rms modules contain the functions used for aligning structures, aligning trajectories, and calculating root mean squared quantities.

Demonstrations of alignment are in Aligning a structure to another, Aligning a trajectory to itself, and Aligning a trajectory to a reference. Another example of generating an average structure from an alignment is demonstrated in Calculating the root mean square fluctuation over a trajectory. Typically, trajectories need to be aligned for RMSD and RMSF values to make sense.

Note

These modules use the fast QCP algorithm to calculate the root mean square distance (RMSD) between two coordinate sets [The05] and the rotation matrix R that minimizes the RMSD [LAT09]. Please cite these references when using these modules.

• Aligning a structure to another
• Aligning a trajectory to a reference
• Aligning a trajectory to itself
• Calculating the root mean square deviation of atomic structures
• Calculating the pairwise RMSD of a trajectory
• Calculating the root mean square fluctuation over a trajectory