A gantry apparatus for a proton treatment system, the gantry apparatus including a gantry wheel and a plurality of adjustable bearings (34,44,64) incrementally spaced apart along an outer diametrical surface of the gantry wheel, a bearing surface configured to receive a portion of the adjustable bearings such that the gantry wheel is supported on the bearing surface by the portion of adjustable bearings received thereon, the gantry apparatus further including a gantry wheel adjustment system wherein the plurality of adjustable bearings are adjustable to compensate for gantry wheel deflection when the gantry wheel is rotated, the gantry apparatus characterized in that the gantry apparatus comprises: a deflection measuring unit configured to measure a deflection value corresponding to deflection of the gantry wheel at each adjustable bearing location when the gantry wheel is rotated; a nominal positioning unit configured to determine a nominal value of gantry wheel compression at each adjustable bearing location according to the deflection value; and an estimation unit configured to estimate a bearing adjustment value for each of the adjustable bearings based on a stiffness parameter of each adjustable bearing to compensate for gantry wheel deflection at each adjustable bearing, where the stiffness parameter is configured as a function of a force applied at each adjustable bearing when the gantry wheel is rotated and a deflection of the gantry wheel associated with the force applied at each adjustable bearing, where the bearing adjustment value corresponds to the nominal position value at each adjustable bearing to compensate for gantry wheel deflection when the gantry wheel is rotated from a first angular positon to a second angular position, the estimation unit being configured to linearly approximate the gantry wheel deflection value by modelling stiffness of the outer diametrical surface of the gantry wheel with springs located radially at each bearing location. a deflection measuring unit configured to measure a deflection value corresponding to deflection of the gantry wheel at each adjustable bearing location when the gantry wheel is rotated; a nominal positioning unit configured to determine a nominal value of gantry wheel compression at each adjustable bearing location according to the deflection value; and an estimation unit configured to estimate a bearing adjustment value for each of the adjustable bearings based on a stiffness parameter of each adjustable bearing to compensate for gantry wheel deflection at each adjustable bearing, where the stiffness parameter is configured as a function of a force applied at each adjustable bearing when the gantry wheel is rotated and a deflection of the gantry wheel associated with the force applied at each adjustable bearing, where the bearing adjustment value corresponds to the nominal position value at each adjustable bearing to compensate for gantry wheel deflection when the gantry wheel is rotated from a first angular positon to a second angular position, the estimation unit being configured to linearly approximate the gantry wheel deflection value by modelling stiffness of the outer diametrical surface of the gantry wheel with springs located radially at each bearing location.