I tried a pertubation run on two proteins. When I look in de full atom score file Rosetta produced, I see rms values that I don't understand. Rosetta for example calculates rms values of 15 A between a decoy and a native. When I recalculate this rms myself in several programs (pymol , vmd) I find values of 5 A. I fitted the largest structure on its native complex. Then I calcuated the rms between the Ca atoms of smallest structures of the decoy and the native. What do I do wrong?
Thanks in advance,