The ability to measure distances within a biomolecule is an important tool for determining structure and function. The electron paramagnetic resonance (EPR) Fourier Convolution-Deconvolution method of measuring distance was utilized to determine the distance between two cysteine mutated residues in the linker region of Sso1p in order to determine the conformation of this region during SNARE complex assembly. A 12 -14 Angstrom distance measurement suggests this region to alpha helical, with a small unstructured area, during complex formation. In addition the limits of distance measurements were tested using the continuous wave electron paramagnetic resonance (cwEPR) method of Fourier Convolution-Deconvolution. This method was unable to measure a known 32 Angstrom distance within the C-terminus region of the SNAP-25 protein.