not sure how the Irms is calculated but I see it as well although I haven’t used the fake_native flag. I think the “rms” column is the Ca rms of the “ligand” unit.
> Hi can you please shed some light on how Irms (reported in the score.fasc file produced as rosetta dock results) is calculated?
> I tried looking at residues of the “ligand protein” that have any heavy atoms within 4 angstroms of the “receptor protein” heavy atoms in the decoy and computing Calpha rmsd shift from the original input versus the decoy. The values I compute are too big by a factor of about 2.
> Please let me know how Irms is defined. Thank you.