- This topic has 4 replies, 2 voices, and was last updated 11 years, 4 months ago by Anonymous.
July 16, 2012 at 8:12 pm #1347Anonymous
When I am looking the energy terms of the fixbb, I find that the rosetta 3.3 has terms as below
> hbond_sr_bb *= 0.5
> p_aa_pp *= 0.5
> rama = 0.2
> omega = 0.5
But 2.3 has only 11 terms.
bk_tot The total score using the design energy function. Lower is better.
fa_atr The attractive portion of the Lennard-Jones? potential. Rewards close contacts.
fa_rep Lennard-Jones repulsive term. Penalizes overlaps.
fa_sol Lazaridis-Karplus solvation model. Penalizes buried polars.
fa_dun Internal energy of sidechain rotamers as derived from Dunbrack’s statistics.
fa_intrares Intra-residue clashes.
fa_pair Statistics based paird term. Favors salt bridges.
fa_prob Probabilistic term: P(aa
hb_sc Sidechain-sidechain and sidechain-backbone hydrogen bond energy.
hb_srbb Backbone-backbone hydrogen bonds close in primary sequence.
hb_lrbb Backbone-backbone hydrogen bonds distant in primary sequence.
Also, I am confused that whether bk_tot is an energy term in rosetta2.3. It seems to me, bt_tot is the sum of packing energy. Thank you for your kindly help!
July 16, 2012 at 8:14 pm #7411Anonymous
bk_tot is not a term in and of itself, it is a summarization of energies used in packing (as opposed to all energies, some of which can’t change during packing, like omega).
3.x represents a reimplementation of the 2.x scorefunction. Some terms are changed in their fine details but in broad strokes it’s the same. We don’t yet have a publication detailing the scorefunction (really, we’ve never had one) but there is one in preparation.
July 16, 2012 at 8:46 pm #7412Anonymous
Thank you very much!
July 17, 2012 at 3:45 pm #7413Anonymous
I check the total score of my designed structure by rosetta 2.3. It shows
But if I use rosetta3.3 score_jd2.default to score the structure, it shows -419.210. If the energy terms and parameters are the same, why the scores are different? Thank you!
July 17, 2012 at 4:14 pm #7414Anonymous
They aren’t the same – “in broad strokes, they’re the same”. The scorefunctions measure the same qualities of the structure (quality of packing, hydrogen bonds, etc), but there are tweaked weights and altered implementations. The two scorefunctions aren’t meant to be compared to one another (or with physical energies, for that matter) – the scorefunctions are primarily useful for ranking within a population of models.
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