You can use Chimera to superimpose.

Using PyMOL, you can extract each chain to separate object and then do alignment.

E.g.

extract chA, myprotein and chain A

extract chB, myprotein and chain B

align chA, chB

myprotein - the name of your pdb file without pdb :)

Thank you all Azadeh Kordzadeh

Can anyone help me how should I select c-alpha, since when we select index file for RMSD what file would it return? Would it return c-alpha or protein?@Shymaa Damfo