I’m confused about the reason for using the top 25 fragments in the library of 200 nine-residue fragments in AbinitioRelax.Instead,for the library of 200 three-residue fragments,all fragments are applied in the process of fragment assembly.
Talking with someone familiar with the protocol, the limitation is because the fragment quality gets worse for the later fragments, and it’s been found heuristically that using fragments beyond the top 25 gives worse results with a reasonable amount of sampling.
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