Reply To: Questions about rosetta fragment library ranking and fragment conformation sampling algorithm

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May 25, 2011 at 11:27 am #5641
Anonymous

    Hi,
    apparently Rosetta always uses the top 25 9-mers. I presume this is the result of ab-initio benchmark. You can however change the default behavior using the -abinitio::number_9mer_frags option, say -abinitio::number_9mer_frags 100 and see what happens in your particular case.

    > Also, is there any further documentation for Fragment picker in the newest Rosetta version?
    > I remember in some previous posts, someone mentioned new picker can deal with various size of fragments besides 3mer and 9mer
    Yes, the new picker allows pick fragments of any arbitrary length; moreover the score function that rules the selection process is fully customizable. I am working to include it in the very next Rosetta release.

    Dominik