Writes the query structure with the atom names, atom order and residue name of the reference, keeping the query's coordinates. The two files must be the same molecule: the atoms are matched by an exact correspondence of the molecular graphs that also preserves the 3D configuration at every stereocentre and double bond, and if no such correspondence exists nothing is written and the reason is shown. Where the molecule's own symmetry leaves a choice, the lowest-RMSD assignment is taken and the interchangeable atoms are listed.

If the reference is an ATB molecule, use the Match to my structure panel on its molecule page instead: it writes every ATB output in your atom order and also checks that the choice among symmetry-equivalent atoms leaves the force-field parameters unchanged.