- This topic has 4 replies, 2 voices, and was last updated 11 years, 4 months ago by Anonymous.
July 29, 2012 at 7:48 pm #1360Anonymous
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!
July 29, 2012 at 8:26 pm #7503Anonymous
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.
July 30, 2012 at 4:45 am #7506Anonymous
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
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
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!
July 30, 2012 at 8:42 pm #7510Anonymous
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.
July 30, 2012 at 9:38 pm #7511Anonymous
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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