alignment.check_sequence_structure() -- check sequence/structure alignment for sanity

check_sequence_structure(gapdist=8.0, io=None)

Output:

n_exceed

This command checks the alignment of the target sequence (the last entry in the alignment) with each of the templates: For all consecutive pairs of ${C}_\alpha$ atoms in the target, it calculates the distance between the two equivalent ${C}_\alpha$ atoms in each of the templates. If the distance is longer than gapdist Å, it is reported. In such a case, the alignment between the template and the target is almost certainly incorrect. The total number of exceeded pair distances is returned.