I've been attempting measure some structures RMSDs by using the PyRosetta's functions all_atom_rmsd() and CA_rmsd(). I've also seen the function native_CA_rmsd(), and used it but I can't tell the diference between this one and CA_rmsd().
So far the functions I use are the ones I've been able to find by tabbing for iPython's autocomplete. I know that there is a native RMSD for all atom, but I've not been able to find it. Are these PyRosetta exposed methods listed somewhere?
Finally, is there a way to measure the RMSD of two structures of different length? I've tried it, but all_atom_rmsd() gives an unidentified C++ exeption.
Thanks in advance.