Reply To: Interface rmsd calculation Irms

[Anonymous]

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.

“SEQUENCE:

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:docking_local_refine
-docking:partners ABCD_EF
-fake_native
-ex1
-ex2aro
-packing:use_input_sc
-docking:dock_mcm_trans_magnitude .4
-docking:dock_mcm_rot_magnitude .2
-mute core.util.prof
-out:output
-out:pdb
-out:file:fullatom
-out:path:pdb ./RESULTS
-out:show_accessed_options

Looking in the file “src/protocols/docking/DockingProtocol.cc” 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/Interface.cc 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.