Supplementary IJulia Notebook for the paper "Structure determination from single molecule X-ray scattering with three photons per image".

In addition to the dependencies below, you will have to install the https://github.com/h4rm/ThreePhotons.jl package (not listed in the Official Julia Repository).

The Crambin data that is analyzed in this notebook is not yet released, but can be reproduced with the job scripts under jobs/run_generate_histograms.jl and jobs/run_parallel_determination.jl.

Content

• Paper.ipynb - Main IJulia notebook with many of the necessary data processing steps. A lot of the code for postprocessing has been put into paper.jl (in the directory) and data_processing.jl in the ThreePhoton.jl package.
• Paper_revision.ipynb - Data processing discussed in the revision of the paper, including experimental data (Coliphage_PR772), multi-particle processing and Ewald sphere approximations.
• Beamstop.ipynm - Calculations concering the beamstop, both in synthetic experiments and real experimental images.

Dependencies

Julia (5.1)

Packages

• IJulia.jl
• PyPlot.jl
• LaTeXStrings.jl
• Seaborn (Matplotlib Package provided via Conda)

You can install the dependencies via:

  ENV["JUPYTER"] = ""
  ENV["PYTHON"] = ""
  Pkg.add("IJulia")
  Pkg.add("PyPlot")
  import Conda
  Conda.add("seaborn")
  Pkg.add("LaTeXStrings")

Running the Notebook

You can run the notebook by executing

using IJulia
notebook() #A browser window should pop up