Reply To: RosettaDesign parameters

> 1. I have several disulfide bonds, so I was trying to preserve them with the -fix_disulf disulf.txt and -norepack_disulf options. As recommended, I tried:
> “rosetta -design -s acdt.pdb -fixbb -ex1 -ex2 -ex2aro_only -ndruns 100 -resfile reslist.res -try_both_his_tautomers”
> All of the scores in the pdb files are around -236 to -230, and the mutants are different, but I guess I am just confused on how to tell which of these mutants are significantly better, if any are.

The command line looks fine. You can simple read the “score” to evaluate the result, lower is better

> 2. By removing -use_bw and using soft_rep, I’ve found that I can get better scores, but they are still not much better than the wild type protein. On that note, how do you score the wild type protein typically? I took the crystal structure and ran design with NATRO in the res file, but I did that several times and get different scores between -236 and -233, which implies that Rosetta is manipulating the structure somehow. And should “score” be the metric by which I compare mutants to the wild type?

It should be the same as long as your resfile’s format is correct. You can also use “-design -fixbb -natrot” command line to score native structure without using resfile

> 3. On the acceptance, if I look at, say acdt_0001.pdb, after the coordinates, I get:
ntrials: 1

%accepted: 0.00
>
> rms_to_start: 2.49374551E-07
>
> score: -235.91
>
> In every generated pdb file, ntrials=1 and %accepted is always 0.00, but the mutants are not the same. When I try to place -ntrials 1000 (for instance) in the rosetta command line, the output is the same (i.e. ntrials=1, %accepted=0.00).

I do not know why the %accepted is always 0 at the moment. You can ignore it.