calculate RMSD

most of the program will superimpose the whole molecule.

some of them give me error message when align our proteins.
ex:Combinatorial Extension (CE) in strap

After all, according to this slides, I use Swiss-PdbViewer .

easy to use by hand, but I'm not sure how to make it calculate RMSD by program automatically.

1. download/load pdb file manually.
2. select residues on the right
3. fit/fit molecule (from selection)
done.