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    I agree that this is likely to be a limitation of the fragment reader.

    It might be possible to tweak the reader itself to support another digit’s worth of residue numbering.

    There is a different system available in 3.1, but it’s not really documented and it’s already been deprecated and replaced in the developer branch. This system lets you pick fragments directly from the Vall (basically a giant fragment database distilled from the PDB). I can give you some code fragments that *might* get you started but I can’t support it more than that…