model to be similar. As we will show, there are sufficient physical processes in our model to illustrate the self-gating pulse effect in single molecule diffraction. All statistical quantities are given as weighted averages over the light elements (H,C,N,O). Sulphur was included in the rate-equations model of damage, but was excluded from the average of statistical diffraction quantities, like $A(q)$, $B(q)$ and $\sigma_B(q)$, because it is computationally intensive. Sulphur has a much larger number of possible electron configurations, and averages that depend on two time variables \[e.g. $\sigma_B(q)$\] took too long to compute for the range of beam conditions we study here. Since there are of the order of 100 sulphur atoms and 10$^4$ light atoms, our main conclusions are not expected to be affected by neglecting the diffraction from sulphur.

We have set up our simulations using the chemical composition and size of GroEL. This chaperonin molecule is a candidate for first tests of single molecule imaging because it survives intact in mass spectrometry experiments[@Rostrom1999], which subject the molecule to similar conditions to injection at XFEL. It is also of sufficient size to scatter around $10^4$ photons per diffraction pattern, as shown in Fig. \[fig:diffraction\_and\_explosion\].

Simulations were performed at 