Structure Format Reference

Page type: Reference

Choose a format by the data that must survive the round trip, not only by file extension.

Format	Coordinates	Periodic cell	Multiple frames	Typical use	Main caution
XYZ	Cartesian	Usually no	Sometimes	Small molecules	Metadata conventions vary
Extended XYZ	Cartesian	Yes	Yes	Calculations and trajectories	Reader-specific property fields
CIF	Fractional/site data	Yes	No	Crystal structures	Disorder, occupancy, and symmetry need review
PDB	Cartesian	Optional	Models	Biomolecular structures	Bonding and element columns can be ambiguous
MOL/SDF	Cartesian and bonds	No	SDF records	Molecular exchange	Charge/stereo support varies
POSCAR/CONTCAR	Direct or Cartesian	Yes	No	Periodic calculations	Element ordering must be preserved
Tako workspace archive	Structures plus project files	Preserved by contained files	Project-dependent	Reproducible handoff	Treat as an archive, not a universal structure format

After import, verify formula, atom count, units, cell vectors, periodicity, coordinates, charge/spin assumptions, and constraints. See Import a Structure.