The Matchmaker utility in Chimera is another good one:

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html

On Sun, Jan 17, 2010 at 12:54 PM, Miri Hirshberg <m...@ebi.ac.uk> wrote:
> Sun., Jan. 17th 2010
> EBI
>
> Greetings,
>
> I am looking for a 3D structure superposition program which takes
> two structures and superpose them based only on the coordinates X,Y,Z
> regardless of of residue/atoms name.
>
> (both files are in PDB format)
>
> Thanks
> Miri

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