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Jaguar is extremely flexible in its input/output options. Taking advantage of the Babel program, Jaguar can accept input in many common file formats and also output results in a variety of file formats.
Jaguar also accepts input geometry in either Cartesian or Z-matrix coordinates, or even a mixed Cartesian/Z-matrix format.
Jaguar supports the use of “dummy atoms” to facilitate geometry input.
Jaguar GUI can render the molecule in a variety of styles, such as CPK, ball and stick, etc.
Jaguar interfaces with other visualization packages such as Spartan or Cerius2 for post-wavefunction visualization of molecular orbitals, electrostatic potentials and electron density surfaces.
The direct interface with Cerius2 was developed with the SDK from MSI, and provides seamless connection between Cerius2 and Jaguar.