May I ask, in what kind of scenario can one ignore the decoy structures but only care about the score? (except there is no harddrive space?) Can one recover the structure later on only from the score? I guess not, right?
-score_only is mostly used when you already have a lot of structures, and are running them through a secondary scoring application (like InterfaceAnalyzer or RosettaHoles). You already have structures and only need scores; re-outputting copies of the structure is a waste of space.
So decoy structures are always recommended to be generated and examined, I guess.
But in the case your described, why not just use score_jd2 to score the structures? It seems by default it only generates Rosetta energy scores.
BTW, what is the difference between commands score_jd2 and score? Sorry I could not find doc on the difference between them and they seem to output the same Rosetta energy score values (I know score generates also rms and gdt scores).