8 keV photon energy ($\sim$0.155 nm wavelength) which is sufficient resolution for structural biology and similar to that demonstrated in simulation studies of single molecule imaging[@Tegze2012]. The principal effects of damage on molecular diffraction can be seen in Fig. \[fig:selfgating\_AB\], which shows a simulation for a pulse duration of 40 fs, beam intensity of $5\times10^{20}$ W cm$^{-2}$ (corresponding to a 2 mJ pulse) and a 100 $\times$ 100 nm$^2$ spot size. Without damage $A(q)$ would be equal to $f_0^2(q)$, but with damage it is reduced, attenuating the mean intensity by the same amount. The attenuation occurs at all resolutions, but is a greater fraction of the original signal at lower resolutions. The term $B(q)$ is lower than $A(q)$ because of the effects of ion motion, and the discrepancy is more pronounced at higher resolution. The deviations between $A(q)$ and $B(q)$ are important for accurate structure retrieval methods[@Quiney2011]. In this case, the most significant damage noise term $\sigma_B(q)$ is lower than $B(q)$ across all resolutions, indicating that even for pulse durations as long as 40 fs damage noise does not exceed the signal from the average molecular structure.

To illustrate the self-gating pulse effect in single molecule diffraction, we plot $B(q)$ 