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    Hi, thanks for the prompt reply. Perhaps the Irms field only shows up in the score file when certain flags are present? I am using the fake_native flag among my input flags. I am including below the first few lines of the score.fasc file produced (sorry about the loss of formatting. the fields should be lined up with total score lining with -1155.903, rms lining up with 2.926….etc) Irms can be found as the 5th field with a value of 1.469.


    SCORE: total_score rms Fnat I_sc Irms dslf_ca_dih dslf_cs_ang dslf_ss_dih dslf_ss_dst fa_atr fa_dun fa_rep fa_sol hack_elec hbond_bb_sc hbond_lr_bb hbond_sc hbond_sr_bb description

    SCORE: -1155.903 2.926 0.585 -3.126 1.469 0.000 0.000 0.000 0.000 -2160.134 126.749 84.863 1012.043 -15.000 -34.537 -94.060 -21.210 -54.618 ./RESULTS//outdir_93/CL0_0122.pdb”

    the flags I am using are:

    -database /usr/global/rosetta/rosetta3.1/rosetta_database
    -l names.txt
    -nstruct 500
    -no_optH false
    -docking:partners ABCD_EF
    -docking:dock_mcm_trans_magnitude .4
    -docking:dock_mcm_rot_magnitude .2
    -out:path:pdb ./RESULTS

    Looking in the file “src/protocols/docking/” I notice on line 470 “score_map_[“Irms”] = calc_Irmsd(pose, *get_native_pose());”

    Later on line 577, calc_Irmsd is defined. I have tried looking through the code here and at src/core/conformation/ but can’t seem to make out how the Irmsd is being calculated. Please let me know what you think. Thanks again for your help.