working with silent output – mergin, clustering and extracting

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    • May 15, 2008 at 12:54 pm #510
      Sally Ride
      Participant

        I would like to run rosetta and analyze its results as following:

        1) Generate decoys in silent format with multiple rosetta runs (that is I have several *.out files)

        2) Cluster all decoys together

        3) Extract structures corresponding to the decoys from best clusters in pdb format

        Sounds easy but:

        * decoys in *.out files from different rosetta runs have the same numbers (in each silent file they start from S_1) so I cannot simply concatenate the files

        * I know rosetta -extract but I would need some simple custom script to get decoys corresponding to the best clusters.

        * I would like to rebuild full atom pdb files

        Has anybody good protocol for that?

      • May 20, 2008 at 2:18 pm #3975
        Anonymous

          Maybe you can change your native pdb to be different name as 1xxxa, 1xxxb, 1xxxc to avoid lose data during extracting silent files.

          > I would like to run rosetta and analyze its results as following:
          >
          > 1) Generate decoys in silent format with multiple rosetta runs (that is I have several *.out files)
          >
          > 2) Cluster all decoys together
          >
          > 3) Extract structures corresponding to the decoys from best clusters in pdb format
          >
          > Sounds easy but:
          >
          > * decoys in *.out files from different rosetta runs have the same numbers (in each silent file they start from S_1) so I cannot simply concatenate the files
          >
          > * I know rosetta -extract but I would need some simple custom script to get decoys corresponding to the best clusters.
          >
          > * I would like to rebuild full atom pdb files
          >
          > Has anybody good protocol for that?

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