How to sort a Silent File based on RMSD

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  • This topic has 2 replies, 3 voices, and was last updated 10 years ago by Anonymous.
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    • August 4, 2013 at 9:40 pm #1683
      Anonymous

        Dear all,

        I have a silent file of 20,000 structures with associated rms for each one. The typical cluster application in Rosetta is not very useful as it clusters them based on energy score.

        1. Simply, I want to sort the structures based on the value of rms from the lowest (best) to the highest (worst), how to do so?

        2. Is there any way to calculate the average of the rms of all decoys?

        Thank you for your time and effort,

        Jad

      • August 5, 2013 at 12:32 pm #9174
        Anonymous

          Hi Jadabbas,
          you can use the score file or you can grep SCORE to get the scores and rmsd values of the decoys from the silent file.
          $grep SCORE x.silent

          Then sort as you want and calculate average rmsd.

        • October 6, 2014 at 10:30 pm #10385
          Anonymous

            I think I know now. :)

            grep SCORE path/to/silent/file | sort -n -k2 > path/to/txt/file

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