Alignments and RMS fitting
Demonstrations of alignment are in align_structure, align_trajectory_first, and align_trajectory. Another example of generating an average structure from an alignment is demonstrated in rmsf. Typically, trajectories need to be aligned for RMSD and RMSF values to make sense.
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.