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. 2016 Apr 25;6:24791. doi: 10.1038/srep24791

Figure 1. Flow diagram of the simS2E pipeline from XFEL pulse generation to the electron density reconstruction.

Figure 1

The FEL source module simulates the electron bunch exiting the undulators using a software package called FAST (Section FEL source). The simulated electron bunch is propagated through the beamline optics to the interaction point using the Prop module using WPG (Section Prop). The PMI module simulates the radiation damage of the protein sample when it is irradiated by the simulated laser pulse using XMDYN (Section PMI). The Diffr module simulates the time-averaged diffraction pattern of the radiation-damaged protein using SingFEL (Section Diffr). The Orient module recovers the orientation of the individual diffraction patterns using EMC (Section Orient) and the Phase module solves the phase problem to recover the electron density using DM (Section Phase).