Fluctuations in I_sc

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    • September 13, 2018 at 7:07 pm #2999
      Anonymous

        Hello,

        I am using “local  refinement” to calculate the I_sc of protein complexes. When I ran Rosetta for the exact same structure multiple times and I got a significant fluctuation in I_SC score, ranging from -2 to -15. This means that in one trial, the complex is unfavorable, but it is favorable in the subsequent trial. What is the reason for this? How can I overcome it? 

        Thank you in advance,

        Emine

      • September 18, 2018 at 4:36 pm #14428
        Anonymous

          Hello,

          That shouldn’t be happening. Are you sure that the poses that are scored are the exact same ones? Minor differences could cause 13 point fluctuations at the interface. Could you share with us the command line options that you used? That’ll help in debugging.

          Thanks,

          Shourya

        • September 20, 2018 at 2:33 pm #14433
          Anonymous

            Dear Shourya,

            Thank you for your prompt response! I also didn’t expect such a huge fluctuation, but this is what I observed. Attached you can find the PPI structure that gave very different results (I am using the exact same structure in multiple runs). The flags that I am using are below:

            For prepack:

            “%s -database %s -s %s -partners %s -ex1 -ex2aro -out:file:scorefile %s/%s_prepeck_score.sc -overwrite -detect_disulf false”

            For local refinement:

            “%s -database %s -s %s -docking_local_refine -partners %s -ex1 -ex2aro -overwrite -detect_disulf false -out:path:score %s”

            Thank you for your help!

            Emine

          • September 21, 2018 at 2:41 pm #14443
            Anonymous

              I am also attaching the score files and the  output structures of 2 runs as an example. 

            • September 21, 2018 at 2:42 pm #14444
              Anonymous

                Here is the second output structure. Although the input structure exactly the same for both runs, the outputs are very different from each other, interms of I_sc and strucutre.

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