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

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May 20, 2011 at 3:55 pm #5615
sokrypton
Participant

    Thank you Dominik!
    That is very helpful!

    In you answer to 3), I’m wondering why Rosetta only uses top 25 ninemers after stage 1. Is it purely for efficiency? Will it reduce the diversity of the fragment conformations being sampled?

    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.

    Thanks!

    Yizhou