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## alignment.check_structure_structure() -- check template structure superpositions

`check_structure_structure(eqvdst=6.0, io=None)`

Output:
  n_exceed

> This command checks the alignment of the template structures (all but the last entry in the alignment): For each pairwise superposition of the templates, it reports those equivalent pairs of atoms that are more than eqvdst Å away from each other. Such pairs are almost certainly misaligned. The pairwise superpositions are done using the atoms and the given alignment. The number of such pairs is returned.

> Note that the target structures are actually changed by the superpositions carried out by this command. If you want to use these superpositions as a crude initial model for `automodel` model building (rather than setting automodel.initial_malign3d) please bear in mind that the later templates in your alignment are always fitted on the earlier templates. Thus, a more reliable initial model will be obtained if you list the higher coverage templates earlier in the knowns variable in your `automodel` script (e.g., always list multimeric templates before monomers).

> If you want to use the original non-superposed structures, either avoid calling this command, or delete and recreate the alignment object afterwards to force it to reread the structure files.

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