where to look for positive sign for solution in mr-rosetta3.4?

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    • July 10, 2012 at 4:38 pm #1340
      Anonymous

        I set up mr-rosetta which is running over 5 days and I guess it should be keep
        running for very long time (ran it on a local machine with single processor.
        260 residues, 1MOL/Asy). My question is where to look for the positive sign:

        So far, the LLG scores from phaser are very low: 2.31-27.1;

        From rebuild:

        Run_1: ROSETTA SCORE: -1273.01;
        Run_2: ROSETTA SCORE: -1427.29;
        Run_3: ROSETTA SCORE: -1468.84
        Run_4: in running

        What would be the good ROSETTA SCORE will possible to lead to the solution?
        How long do you think mr-rosetta could keep running?

        Thanks!

      • July 10, 2012 at 5:52 pm #7393
        Anonymous

          I can’t answer your question without knowing a lot more about the system. Using the regular Rosetta scorefunction, about -2 units per residue is “good”, so -520 would be an acceptable score. You’re well better than that, which might be good. However, I have a feeling this code isn’t using the standard Rosetta scorefunction.

          The only true answer for “how long should it run” for a Monte Carlo protocol is “until you like the answer” – can you look at Run 1-3 and see if they fit your needs?

        • July 11, 2012 at 3:35 pm #7396
          Anonymous

            Thanks smlewis. The score I took was from Stage “GROUP_OF_ROSETTA_REBUILD_1”:

            rosetta_solution ROSETTA SCORE: -1483.00

            But in the same log file, it also indicated:

            component_solutions: None

            So I was not so sure what is good or bad.

            Since I was running in a local machine with single processor only, it will run forever (over a month). So I took one of the best over_best solution (pdb and mtz files), then run phenix.autoBuild, but the results was not good: R=0.49, Rfree=0.56. This is not going to be the right solution.

            What should I do next?

            Thanks!

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