I think Rosetta calculates the rms of a complex in a different way. It aligns the whole decoy complex over the native complex by superimposing the center of masses of both the complexes. Then rotates the decoy to get the best alignment with the native structure. Then RMSD is calculated.
While in your method, you have superimposed the bigger structure over the native one and the RMSD for that unit will be ~0. Whatever RMSD you get comes only from the smaller unit of the complex. Apart from that pymol also tends to get rid of some residues which do not align and give RMSD of only those residues which align to some extent. You will see following comment on pymol
“34 atoms rejected during cycle 1” etc…
Hope that helps.
> 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,