I used the loop protocol to generate ab int loop and I found that there is no scoring information for the loop models and I don’t know how to judge which one would be the best one. Could you please give me some advices? Here is my flag parameters:
If it didn’t put scores in your output PDBs, and it didn’t put scores in a scorefile, then you can generate scores with the score app (score.cc, score.???release). It will load the PDBs and print scores for you. It’s quite fast.