I'm looking for the easiest way of calculating RMSD between two homologues proteins. (i.e. sequences do not match perfectly). Until now I was using Chimera software, where steps are as follow:
1. Calculating pairwise alignment
2. Then structures are superimposed
3. RMSD is calculated between corresponding amino acids in alignment.
And this work quite well, but I'm looking for something simpler that I can use in python script. Preferably in with no need of running subprocess.