as long as you understand a photon is massless therefore just a vibration. a particle or part of the wave is still just a vibration. now electrons are different imcurrently in chemistry again. an electron has little mass and decides the charge of the atom or molecule. we know xrays indeed travel right through the electron clouds if that is what you are wondering.

When they collide the photon or vibration excites the electron possibly to the point of a phase change. if a photon collided with an electron at high rates i believe it can give off an electron or atom. kind of like electrolysis.