the energy terms in fixbb

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    • #1360

        Dear developers,
        It says in rosetta2.3 manual
        “The main score is Wbk_tot * bk_tot + Wother * other. The other terms that contribute to the score evaluate the backbone stucture, e.g. the ramachandran score. The score is supposed to be the energy with bk_tot as just one part of it. For the sake of consistency, the score can be used instead of bk_tot when thinking of the quality of output structures”
        Can anyone tell me what are the other terms in the fixbb scoring function? Thank you!

      • #7503

          Your best bet for understanding the 2.3 energy function (which is no longer actively developed) is to read Kulhman’s 2003 (?) top7 paper in Science; especially the supplemental information. Secondarily you should read the Rohl review in Methods in Enzymology which covers the genesis of a lot of the energy terms.

        • #7506

            Thank you! I have read their paper but still not clear about the detail.
            I run the rosetta2.3 fixbb and got the result as
            ntrials: 1
            %accepted: 0.00
            rms_to_start: 3.20122297E-07
            score: -128.57
            env: 19.19 env_weight: 0
            pair: -24.21 pair_weight: 0
            vdw: 0.00 vdw_weight: 0
            hs: 0.00 hs_weight: 0
            ss: 0.00 ss_weight: 0
            sheet: 0.00 sheet_weight: 0
            r-sigma: 0.00 r-sigma_weight: 0
            cb: 22.18 cb_weight: 0
            rg: 11.41 rg_weight: 0
            co: 11.54 co_weight: 0
            contact_pred: 0.00 contact_weight: 0
            rama: -4.08 rama_weight: 0.2
            hb_srbb: -54.94 hb_srbb_weight: 0.5
            hb_lrbb: -2.55 hb_lrbb_weight: 1
            bk_tot: -161.35
            fa_atr: -247.34
            fa_rep: 28.76
            fa_sol: 120.17
            fa_h2o_sol: 0.00
            fa_dun: 45.92
            fa_intrares: 0.05
            fa_pair: -9.18
            gb_elec: 0.00
            fa_plane: 0.00
            fa_prob: -12.28
            fa_h2o: 0.00
            fa_h2o_hb: 0.00
            fa_ref: 24.58
            gsolt: 46.10
            sasa: 5088.18
            hb_sc: -5.40
            sasapack: 2.02

            I don’t the what makes the score=-128.57. It seems that the
            score= bt_tot_weight*bk_tot + rama_weight*rama + hb_srbb_weight*hb_srbb +hb_lrbb_weight*hb_lrbb
            But these terms doesn’t end up to -128.57. Could you please show me how the score is calculated? Thank you very much!

          • #7510

              None of our developers have used 2.3 in several years, and the answer I’m consistently getting is “well, um…I don’t remember how it works”.

              If you want a useful breakdown of scores for the structure you have, I will enthusiastically suggest you use Rosetta 3.4 instead – you can just score the structure you already have with score_jd2, and those will add up properly.

            • #7511

                Yes. Rosetta3.4 score_jd2 can do that. I just don’t understand what makes the different between rosetta2.X and rosetta3.X. Thank you very much!

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