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src/m/d/MDAnalysis-0.8.1/examples/rmsfit_qcp.py   MDAnalysis(Download)
    ts._pos[:] = ts._pos * R # R acts to the left & is broadcasted N times.
    ts._pos   += ref_com
    writer.write(traj.atoms) # write whole input trajectory system
 
numpy.savetxt('rmsd.out',rmsd)