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    hmm, sorry to be back again so soon but now I think i’ve discovered another problem with this approach.

    Unfortunately my complex is more than 999 residues long and as far as I can work out this makes it incompatible with the fragment file format
    assuming that in the line:

    position: 127 neighbors: 200

    the “position:” here is the residue index

    and that it is specified also here:

    3bam A 201 R L -93.490 -14.266 -179.524 0.018 4.874 22.272 4 0.000 P127 F 8

    where it says “P127”

    But even after I have set up fragments that I think correctly correspond to parts of the complex I would like to remodel I still get the error:

    protocols.abinitio.FragmentMover: couldn’t find fragment to insert!!

    so I think the easiest thing I can do is model each chain separately and then put them back together at the end.