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    1) All you have to do is ensure that the two sides of your interface end up in different sub-Poses (the ones called E2 and E3_RING in the original code). It will work equally well no matter which of those two the flexible tail ends up in. The fact that your tail is N-terminal makes no difference.

    I suggest un-commenting-out (commenting-in?) these lines:
    //JobDistributor::get_instance()->job_outputter()->other_pose( job_me, E2, “E2”);
    //JobDistributor::get_instance()->job_outputter()->other_pose( job_me, E3_RING, “E3_RING”);
    These will print copies of the sub-poses to PDBs with the appropriate names to let you test if the split occurred the way you wanted it to. Once it works you can take these two lines out again.

    2) FloppyTail uses only 3-mer fragments. It takes whole-pose fragments, such as those generated by the Robetta server ( (The vast majority of the fragment file is never used, which is kind of wasteful. Rosetta’s fragment machinery implicitly assumes you are doing abinitio, whole-structure folding so it forces you to supply a full fragments file.)

    I found fragments to be unimportant for the Cell paper, but it might matter if your tail is expected to have significant secondary structure. I can’t tell you if it will matter or not; you’ll have to try it both ways.