pulse energy. We propose the following signal-to-noise ratio to characterize the diffraction: $$\begin{aligned}
SNR_{ND}(q)  = \frac{N B(q)}{\sqrt{N \sigma^2_A(q) + N^2 \sigma^2_B(q) + N \sigma^2_N(q)}} \;.
\label{eq:SNR}\end{aligned}$$ It is also interesting to compare the signal to the damage noise directly, ignoring shot-noise, with the following ratio: $$\begin{aligned}
SNR_D(q)  = \frac{N B(q)}{\sqrt{N\sigma^2_A(q) + N^2\sigma^2_B(q) }} \;.
\label{eq:SNRD}\end{aligned}$$ To estimate $SNR_{ND}(q)$ and $SNR_D(q)$, we need to calculate statistical averages of the scattering factor, e.g. $\langle f(q,t) \rangle$, $\langle f^2(q,t)\rangle$ etc, which in turn depend on the expected number of ions in each ionization state as a function of time. To calculate $B(q)$ and $\sigma_B(q)$ we also need to know the ion temperature as a function of time. These parameters can be calculated by many of the damage models reported in the literature so far, like molecular dynamics models [@Neutze2000; @Jurek2004b] and hydrodynamic (rate-equations) models[@HauRiege2004; @Scott2001; @Caleman2011]. Here we will present the results of a rate equations model to investigate single-molecule diffraction contrast and to explore the extent to which there is a self-gating pulse effect in single molecule diffraction.

The term that has not been calculated before is the correlation between the scattering factor at different time points, e.g. $\langle f(q,t) f(q,t')\rangle$, which 