printing our per-residue energies including H-bonding energies

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    • July 2, 2013 at 3:51 pm #1634
      Anonymous

        Hi all

        Could anyone help me out in figuring out a way for printing out per-residue energies including the “hydrogen bond energies” using Rosetta 3.4. It sounds that the per residue energies obtained at the end of the annotated PDB files doesn’t includes the hydrogen bond energies, as Rosetta stores H-bonding energies only on a per-pose basis. This results in inconsistencies between the sum of per residue energy and the total energy reported by Rosetta.

        Thanking in advance

        Regards,
        Vijayan.R

      • July 15, 2013 at 6:16 pm #9053
        Anonymous

          Hi Vijayan,
          You can use per_residue_energies.linuxgccrelease which print the energies per residue as

          SCORE: pose_id fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih dslf_ca_dih rama omega fa_dun p_aa_pp ref score description
          SCORE: 1.pdb -1.875 2.173 0.655 0.011 1.471 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.039 0.000 0.290 2.765 residue_1
          SCORE: 1.pdb -3.324 0.592 0.962 0.001 1.487 0.000 0.000 -0.831 0.000 0.000 0.000 0.000 0.000 0.000 -0.289 0.762 0.395 -0.562 0.020 -0.787 residue_2

          Is that what you’re looking for?

        • July 16, 2013 at 12:25 am #9062
          Anonymous

            per_residue_energies is an unreleased pilot app, so wouldn’t be available unless you have the internal developers source. I don’t believe there’s a way to access that information in the release version without recompiling.

            A quick fix is to edit score_jd2 to insert the following lines to the file (not-tested: line numbers given for reference, and might not be exact.), recompile, and then run the score_jd2 application on your structures with the -out:pdb option. This should have the backbone H bonding breakdown in the output PDB.:

            00029 #include <core/scoring/Energies.hh>
            00030 #include <core/scoring/ScoreFunction.hh>
            +++ #include <core/scoring/methods/EnergyMethodOptions.hh>
            +++ #include <core/scoring/hbonds/HBondOptions.hh>
            00031 #include <core/scoring/ScoreFunctionFactory.hh>
            00032 #include <basic/options/option.hh>

            …

            00147 sfxn_->set_weight( core::scoring::linear_chainbreak, 4.0/3.0 );
            00148 sfxn_->set_weight( core::scoring::overlap_chainbreak, 1.0 );
            +++ core::scoring::methods::EnergyMethodOptionsOP emopts( new core::scoring::methods::EnergyMethodOptions( scorefxn->energy_method_options() ) );
            +++ emopts->hbond_options().decompose_bb_hb_into_pair_energies( true );;
            +++ scorefxn->set_energy_method_options( *emopts );
            00149
            00150 if ( ! skip_scoring_ ) {
            00151 (*sfxn_)( pose );
            00152 }
            00153 }

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