[BioPython] Structural alignment

[Omid Khalouei]

Hello,

I was wondering what's the current common practice to align two different 
structures belong to the same protein. In particular I want to align two 
HIV-1 protease structures obtained from PDB and get the RMSD. I know how to 
do this with Swiss-PdbViewer, using the "majic fit". In a paper they have 
done this with the program MOLMOL but I am having difficulty installing it 
on my Windows computer since the program is meant to be used by Linux/Unix 
machines.
Are there any other efficient publicly available tools for this purpose?

Thanks for your help,
Omid K.