Hi,
I'm analyzing the clashing between the residues of my protein and want to obtain a list of fa_rep scores for each of the residues of this protein. The thing is, when I score the model with rosetta_jd2 protocol the score of fa_rep that I obtain for the residues I'm interested in are around 0-3 REU and are not different from the rest of the structure. However, when I look at this protein in Foldit Standalone the fa_rep scores that I obtain for those residues are around 150-300 REU, while the rest of the molecule shows numbers of 0-5. I'm trying to understand where these discrepancies come from. IN the Foldit documentation they indicate that the scores are obtain from the ref2015 energy function of rosetta and that they may use some filters (which they don't describe).
The differences make sense to me, but I want to obtain similar results scoring directly through rosetta. How can I do that?
Thanks.