Construction of a tripeptide from a mol2chemfig-generated aminoacyl residue. The file containing the coordinates for a phenylalanyl residue was rendered to a ∖submol definition, and three copies of the latter were concatenated. In A, mol2chemfig was allowed to arbitrarily pick the first and last atoms of the sub-molecule’s main chain, which causes the connecting bonds to be misplaced. In B, the atom numbers of the molfile were displayed using the -n or --atom-numbers option. In C, atoms 6 and 11 were specified as the main chain entry and exit points, respectively; this causes the connecting bonds to be placed as intended. In the generated code, the amino group was manually adjusted.