A novel tool has been developed to automate the process of locating the isocenter, center of rotation, and sphere of confusion of a proton therapy gantry. The tool uses a Radian laser tracker to estimate how the coordinate frame of the front-end beam-line components changes as the gantry rotates. The coordinate frames serve as an empirical model of gantry flexing. Using this model, the alignment of the front and back-end beam-line components can be chosen to minimize the sphere of confusion, improving the overall beam positioning accuracy of the gantry. This alignment can be performed without the beam active, improving the efficiency of installing new systems at customer sites.