Ab initio/relax flag file setup

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    • August 28, 2009 at 6:49 pm #355
      Anonymous

        Hi,

        Does anyone know if the the Rosetta 3.0 release structure prediction Flag file requires one of the three types of secondary structure files (i.e Jones . etc) as input in order to run properly? I do not have a native pdb file to provide as input. However, I was able to run the program without any issues with only the FASTA sequence file, and the fragment libraries as input, to generate an ensemble. I am concerned that the decoys generated without a secondary structure file present will not be useful.
        I have attempted to input one of the three secondary structure files into the flag folder but the program fails to recognize it (likely because I am probably not calling it with the correct cmd, etc?) and won’t run.

        Thank you for reading this.

      • August 28, 2009 at 9:30 pm #4161
        Anonymous

          same situation here. Have to guess what to do. Not really sounds like doing science(:razz:)

          > Hi,
          >
          > Does anyone know if the the Rosetta 3.0 release structure prediction Flag file requires one of the three types of secondary structure files (i.e Jones . etc) as input in order to run properly? I do not have a native pdb file to provide as input. However, I was able to run the program without any issues with only the FASTA sequence file, and the fragment libraries as input, to generate an ensemble. I am concerned that the decoys generated without a secondary structure file present will not be useful.
          > I have attempted to input one of the three secondary structure files into the flag folder but the program fails to recognize it (likely because I am probably not calling it with the correct cmd, etc?) and won’t run.
          >
          > Thank you for reading this.

        • August 28, 2009 at 9:35 pm #4162
          Anonymous

            The “-nooutput” in cluster did not work for me, so be careful when you try your LUCK for that part before you fill up your hard disk.

            > Hi,
            >
            > Does anyone know if the the Rosetta 3.0 release structure prediction Flag file requires one of the three types of secondary structure files (i.e Jones . etc) as input in order to run properly? I do not have a native pdb file to provide as input. However, I was able to run the program without any issues with only the FASTA sequence file, and the fragment libraries as input, to generate an ensemble. I am concerned that the decoys generated without a secondary structure file present will not be useful.
            > I have attempted to input one of the three secondary structure files into the flag folder but the program fails to recognize it (likely because I am probably not calling it with the correct cmd, etc?) and won’t run.
            >
            > Thank you for reading this.

          • August 31, 2009 at 2:17 pm #4164
            Anonymous

              I can’t say for sure but I think you should be safe. The fragment libraries are created from secondary structure prediction, and so the fragments themselves encode the local secondary structure preferences. I don’t see an obvious option for including your own ss file either (except for defining where the loops are yourself).

            • August 31, 2009 at 3:26 pm #4165
              Anonymous

                Ok great…and the results I am getting in the output do seem to match the secondary structure provided by the three seperate secondary structure files.

                Thank you for your reply

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