The esiest way to get familiar with HYDROID is to follow one of the well documented stage-by-stage examples and modify them as needed for the user data:

• Example 1: Quantifying HRF of a centromeric nucleosome with DNA radioactively labeled at 3' end. Predicting cleavage frequency profiles from an atomistic structure model and comparing to experimental ones.
• Example 2: Quantifying HRF of a nucleosome with DNA radioactively labeled at 5' end. Highlights conversion of gel images to data profiles via ImageJ.

Additionally an example for calculating H-SASA profiles from molecular dynamics trajectories is provided: see ExampleMD.