The names of the chains in a PDB file are arbitrary. For example, considering the two tetramers depicted, chains may be labeled clockwise in one PDB file but counter-clockwise in another. Thus, although two structures can be similar structurally, differences in chain order can yield a false negative result when structures are being compared. To circumvent this problem, we must infer chain-chain correspondences among the structures being compared. This was achieved using a seed superposition of the two structures, which is based on chains from the first QS maximizing the TM-score with the second QS. If the QSs are similar, this seed superposition naturally places structurally equivalent chains in proximity, which made their identification possible by analysis of the aligned coordinates. We then used this mapping to re-write the coordinate files in matching chain order, and recalculated a global superposition of the complete QSs using the re-ordered coordinates. The latter provided us with the final TM-score.