Technically, a template with a neutral terminal NH 2 would find three subgraph matches and copy a neutral charge to the nitrogen. However, when explicit degree matching is given, only the correct terminal NH 3 + monomer template is queried in the PDB topology. 5. Any set of monomers should not contain monomers whose overlapping regions (defined by the atomic number and connectivity only) contain conflicting resonance structures such as in Figure . Such cases are rare and are impossible to rectify automatically given the limited information in PDB files. However, the strength of a manually specified monomer format over traditional bond guessers is the ability to catch such ambiguous cases rather than silently erroring.