  Understanding the physical structure of the planet formation environment, the
protoplanetary disk, is essential for the interpretation of high resolution
observations of the dust and future observations of the magnetic field
structure. Observations of multiple transitions of molecular species offers a
unique view of the underlying physical structure through excitation analyses.
Here we describe a new method to extract high-resolution spectra from
low-resolution observations, then provide two case studies of how molecular
excitation analyses were used to constrain the physical structure in TW Hya,
the closest protoplanetary disk to Earth.
