Hi Rosetta people
I have an odd problem concerning the interface rmsd output from rosetta dock.
I have two structure outputs from different runs. Only difference is using saxs as restrain in one run otherwise the scripts are identical.
I get better irmsd from the saxs run (0.333 vs. 1.116) but when looking at the structures there is barely any difference, I have checked rotamers as well.
I have looked at the fold tree to see if there is a problem in interface recognition between the two. The residues number for the jump is set as the center of each protein (that is center of protein, center of "ligand"). As I understand it there is no problem.
I use the "-native" flag too identify the native structure for rmsd calculation.
I cannot figure out how Rosetta would evaluate these two structures different?
Any chance you have a clue for where to look for the problem???
I don't seem to be able to upload the PDB files or log file as the exceed the file size allowed by your server.