generating 10 lowest energy structures from abinitio

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    • May 7, 2010 at 6:44 pm #577
      Anonymous

        Hi
        I ran the abinitio protocol for a protein with its fasta sequence only. I generated the fragments using the Robetta server. I got only 1 pdb file as an output. How do I get it to generate 10 lowest energy structures in pdb format?
        Thanks.

      • May 10, 2010 at 1:49 pm #4448
        Anonymous

          did you try -nstruct 10?

        • May 27, 2010 at 5:01 am #4457
          Anonymous

            Dear Rosetta devs and community,

            What does Robetta use for decoy selection, and is this method codified in any protocols in the Rosetta3.1 source? I’ve generated a large set of structure decoys using AbinitioRelax, and I’d like to select the top 5 decoys. I can attempt to reproduce the clustering method described in Bonneau et al {JMB (2002) 322:65-78}, but is this the latest and greatest approach?

            Thanks much,
            Nasos

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