I am docking an antibody to antigen using the snugdock server. Just wanted to know whtat is the reference structure in the the RMSD deviation in the score.sf files. Is it the structure with the lowest rosetta energy. In case if you want to compare the original structure of complex with decoy structure what is the easiest option. i am attaching the gnuplot out put of the Total Score Vs RMSD . Any help would highly be appreciated
Dr. Suji george
The reference structure is the input or the initial complex. If you want to recalculate your rmsd/score, then the best way to is to download the models from ROSIE and run docking_protocol locally:
See the last bullet here: https://www.rosettacommons.org/docs/latest/application_documentation/docking/docking-protocol#tips.