the energy terms in fixbb

[Anonymous]

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!

[Anonymous]

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.

[Anonymous]

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!

[Anonymous]

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.

[Anonymous]

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!

[Author]

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