On Thu, Jul 9, 2009 at 2:56 PM, Keren Lasker<> wrote:
> On Jul 10, 2009, at 12:33 AM, Daniel Russel wrote:
>> - The names should be more the questions that come up for me are
>> Â(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).