At submonolayer coverage, Mn forms atomic wires on the Si(001) surface oriented perpendicular to the underlying Si dimer rows. While many other elements form symmetric dimer wires at room temperature, we show that Mn wires have an asymmetric appearance and pin the Si dimers nearby. We find that an atomic configuration with a Mn trimer unit cell can explain these observations as due to the interplay between the Si dimer buckling phase near the wire and the orientation of the Mn trimer. We study the resulting four wire configurations in detail using high-resolution scanning tunneling microscopy (STM) imaging and compare our findings with the STM images simulated by density functional theory. © 2012 American Physical Society.