Basic example

A typical usage pattern is to iterate through a trajectory and analyze coordinates for every frame. In the following example the end-to-end distance of a protein and the radius of gyration of the backbone atoms are calculated:

    import MDAnalysis
    from MDAnalysis.tests.datafiles import PSF, DCD   # test trajectory
    import numpy.linalg

    # load trajectory and topology into a Universe
    u = MDAnalysis.Universe(PSF,DCD)  
    # from the 4AKE segid, select
    # the first atom named N and the last atom named C
    nterm = u.select_atoms('segid 4AKE and name N')[0]
    cterm = u.select_atoms('segid 4AKE and name C')[-1]
    # select the backbone atoms (AtomGroup)
    bb = u.select_atoms('protein and backbone') 

    for ts in u.trajectory: # iterate through all frames
        r = cterm.position - nterm.position # end-to-end vector from atom positions
        d = numpy.linalg.norm(r) # end-to-end distance
        rgyr = bb.radius_of_gyration() # method of AtomGroup
        print("frame = {0}: d = {1} A, Rgyr = {2} A".format(
              ts.frame, d, rgyr))

To find out what else you can do, head over to learning MDAnalysis to have a look at the tutorials and the docs.