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    … actually, it’s the other way around. “assert( len(argv)>2)” is the line which is raising the AssertionError, and the assertion error is raised because the thing passed to assert is false. That is, len(argv) is not greater than two – the code expect to have two or more command line parameters (one of the entries in argv is the script name).

    Specifically, it looks like the script expects the first command line parameter to be the pdb name, and the second to be the chain ID. Parameters 3 and up can include ‘-nopdbout’, ‘-nochain’ and ‘-ignorechain’ (it looks like anything else is ignored). Flags have to be at position 3+; putting the option flags before the pdb name and chain ID will not work.