I think it would be very helpful if each ROSIE docking2 job would output the scores for the input pdb file (proteins.pdb) in its score.sf file and spreadsheet, just like it now outputs the scores for all the other pdb files (proteins_*.pdb) it calculates. The graphs could include points for the input pdb file as well, which I think will always give rms or RMSD values of 0. Listing and graphing values for the input pdb file would help check results if one takes a pdb file output from one ROSIE job and uses it as input to another ROSIE job. One could also compare the total_score with rms=0 to the best total_score to see if docking2 has improved the total_score.
One could also more easily check if different types of ROSIE jobs (like docking2 vs symmetric_docking) score things the same way. For example, one could take a pdb file output from a ROSIE symmetric_docking job for a cyclical hexamer, put a TER line between a pair of its subunits, and use this pdb file as input to a ROSIE docking2 job. Would the initial docking2 total_score match that reported by the symmetric_docking job? Would I_sc/6 for the hexamer in the symmetric_docking job match the initial I_sc/2 score for the hexamer in the docking2 job?
If you graph the values for the input pdb file, please mark its points with special colors or shapes.