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If you just want the mathematics and are willing to roll your own code, you can use the method of Wolfgang Kabsch. I see this has been enshrined in a Wikipedia page at http://en.wikipedia.org/wiki/Kabsch_algorithm This is what I've used when I've wanted to superimpose points where the mapping between the points is defined. If the points in your tetramer aren't pathological, like lying in a common plane, you shouldn't have to worry about SVD and can just perform the matrix inversion. Dale Tronrud On 12/27/12 11:16, Waugh, David (NIH/NCI) [E] wrote: > Greetings, > > I have what seems like a relatively simple problem to solve, but have not been able to do so using the software tools I know about. I have two sets of 4 points in 3D space (atoms in PDB files). They represent equivalent positions in two tetrameric proteins. I would like to align these points in one PyMol or Coot file. I don’t want a NEW set of points representing the LSQ average of the two sets, which is what I get in Coot’s SuperPose. Instead I am looking for a way to “superimpose” one atom from each set and then rotate one set for the best fit. I’m not an intuitive expert on symmetry, but I think there is probably only one best solution to this problem, right? I also need the atomic distances to be on the same scale in the two sets of points. > > Thanks for any help! > > Dave Waugh > > -- > David S. Waugh, Ph.D. > Macromolecular Crystallography Laboratory > Center for Cancer Research > National Cancer Institute > Bldg. 538, Room 209A > Frederick, MD 21702-1201 > +1 (301) 846-1842 > [log in to unmask] > http://mcl1.ncifcrf.gov/waugh.html > --