3D Protein Alignment - description from Softdepia.com:
If you have a PC with DOS or Windows 95/98/NT and want to compare 3D structures of proteins (in PDB format) this program is for you. The program does not need any sequence gomology and any previous assumption about 3D structure similarities of starting proteins. The program can determine itself the degree of 3D similarity. The output are 3D coordinates of second protein rotated and shifted to the best fitting to coordinates of the first protein in PDB format. You can see and manipulate stereoscopic images of starting structures and final result, using mirror stereo-glasses. The second kind output is the linear representation of 3D alignment and the list of structure conservative regions that fit to given RMS deviations.
3D Protein Alignment is a "Free to try" program. You can download and try it for an evaluation period.