Reply To: Interface rmsd calculation Irms

[Anonymous]

I can’t find an lrms field in the normal scorefile. The rms field is filled by a function called “calc_Lrmsd”, so I’m guessing that’s what you mean?

The function appears to be defined at line 557 of src/protocols/docking/DockingProtocol.cc. Its internal comments do not shed much light. It appears to get the RMSD of the entire mobile side half the dimer against its position in the “native pose” – it’s not limited to interface residues. Does this solve your problem?

> 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.