Manganese self-assembles into atomic chains on the Si(001) reconstructed surface. Our combined scanning tunneling microscopy, atomic force microscopy (AFM) and density functional theory (DFT) study revealed a simple necklace-like structure of the Mn chains. The DFT calculated adsorption energies support a single Mn atom adsorption H' site, however no gain in energy promoting the formation of chains was found. We use atom manipulation techniques to deconstruct the chains and confirm the H' site model. Moreover, we show that the manipulated atoms dissipate energies, in the damping channel of AFM, that can be compared to the diffusion energies from DFT calculations.