On Thu, Jul 9, 2009 at 2:56 PM, Keren Laskerkerenl@salilab.org wrote: > > On Jul 10, 2009, at 12:33 AM, Daniel Russel wrote: > >> Comments: >> - The names should be more the questions that come up for me are >> (1) if it is coordinate RMSD, are the molecules rigidly aligned >> before it is computed (and with the hierarchies case, are they all >> aligned together or separately) > > yes - this is a very simple function that assumes correspondence between the > two structures. > Solving the correspondence problem should be handled n a different function Correspondence and rigid alignment are different questions. Correspondence is hard enough to solve that I figured it was clearly not being solved. Rigid alignment is trivial so it is not unreasonable to assume it is done (but unclear whether or not it is).