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    Unrecognized residues (like HSD for HIS) should lead to “unrecognized residue” errors, not segfaults.

    The list of possible flaws in PDBs that can cause segfaults is both long and unenumerated. The last time someone had an error, it was because all their occupancies were 0 – if your whole occupancy column is 0 for all residues it is likely to cause this problem.

    A) compile in debug mode; run in debug mode (or even in the debugger), post the error then (it’s 99% chance an uninformative vector overrun, requiring the debugger)

    B) post the PDB here (there’s a file attach option) and I’ll look for obvious flaws.

    EDIT: I didn’t realize this was in the pyrosetta forum – I guess you can’t do debugging?