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!
Post Situation:
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.
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!
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.
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!