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A Julia package for the structure determination from single molecule X-ray scattering experiments with down to only three photons. This package has not been officially released in the Julia Repository.

This is not meant for 'out-of-box' usage (yet). It is a proof-of-principle demonstration of the method described in the paper "Structure determination from single molecule X-ray scattering with three photons per image".

Installation

First, clone the repository:

  git clone https://github.com/h4rm/ThreePhotons.jl.git

Then make sure the environment variables are set correctly:

  #Make sure julia finds the module
  export JULIA_LOAD_PATH=/path/to/ThreePhotons.jl/src
  #Make sure the s2kit is found
  export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/path/to/ThreePhotons.jl/src/sh
  #Tell julia where the structure determination runs
  export THREEPHOTONS_PATH=/path/to/ThreePhotons.jl/

Next, compile s2kit and the s2kit interface (part of this framework):

  cd src/sh
  make

Starting from a fresh Julia installation, you may run:

  Pkg.init()
  Pkg.add("CUDArt")
  Pkg.add("Distributions")
  Pkd.add("ProgressMeter")
  Pkg.add("Optim")
  Pkg.add("CurveFit")
  Pkg.add("PyPlot")

to initialize Julia with all required packages.

Package Functionality

The package implements three major aspects of the structure determination method:

  • 3D description of electron densities, Fourier densities and intensities
  • synthetic image data generation and subsequent histograming of the two- and three-photon correlation
  • structure determination runs starting from correlation histograms

Description of 3D Structures with Spherical Harmonics Basis

This package provides functions to describe 3D structures on a cubic grid or on a spherical grid, each shell expanded in spherical harmonics. PDB structures can be loaded directly.

  using ThreePhotons

  LMAX = 25 #Maximum expansion order of spherical harmonics expansion
  KMAX = 30 #Maximum number of shells used in the expansion

  #Description of the Crambin electron density, Fourier density, and Fourier intensity expanded in Spherical Harmonics
  density,fourier,intensity = createSphericalHarmonicsStructure("data/structures/crambin.pdb", LMAX, KMAX, float(KMAX))
  #Same Crambin structure on a cubic grid
  densityCube,fourierCube,intensityCube = createCubicStructure("data/structures/crambin.pdb", 2*KMAX+1, float(KMAX))

Synthetic Scattering Images And Histogramming

This package covers the generation of synthetic scattering images (with and without noise) and subsequent two-photon and three-photon histogramming. For computational reasons, the scattering images are not cached.

  using ThreePhotons
  include("jobs/runs.jl")

  generate_histograms(;
    num_images        = Integer(1e6), #Number of images to generate,
    max_triplets      = Integer(0), #Alternatively, the maximum number of triplets can be limited
    Ncores            = 8, #Number of CPU cores used for the data generation
    N                 = 32, #Alpha/beta discretization
    photons_per_image = 10, #Photons per image
    batchsize         = round(Int64,1e6/8),
    successive_jobs   = 1,
    use_cube          = false, #Use cubic or spherical harmonics description for data generation
    qcut_ratio        = 1.0, #Fraction of maximum wave number
    K                 = 38, #total number of shells
    rmax              = float(38), #maximum radius in real space
    histogram_method  = "histogramCorrelationsInPicture_alltoall",
    structure_pdb_path= "data/structures/crambin.pdb"
  )

jobs/runs.jl includes helper functions to spawn data generation and structure determination runs in various environments (including cluster systems).

Structure Determination

Given a histogrammed two- and three-photon correlation, the structure can be retrieved de novo:

  using ThreePhotons
  include("jobs/runs.jl")

  num_images::Int64 = Integer(1e6) #number of images
  KMAX::Int64       = 38 #Maximum shell number used for two-photon inversion
  N::Int64          = 32 #Alpha/beta discretization
  L::Int64          = 18 #Maximum expansion order
  K::Int64          = 26 #Number of shells used for structure determination
  ppi::Int64        = 10 #Photons per image used for the histogram
  rmax              = float(KMAX)#Maximum radius of the reference structures
  name              = histogram_name("", ppi, N, KMAX, float(KMAX), img, "") for img in image_list) #histogram file name

  run_determination(
    "runname", #Name of the run
    histograms              = name, #Path to the histogram file

    #Expansion parameters (see above)
    K                       = K,
    L                       = L,
    KMAX                    = KMAX,
    rmax                    = rmax,
    N                       = N,

    #Monte Carlo simulated annealing parameters
    initial_stepsize        = pi/4.0,
    optimizer               = "rotate_all_at_once",
    initial_temperature_factor=0.1,
    temperature_decay       = 0.99998,
    stepsizefactor          = 1.01
    measure                 = "Bayes",

    #Misc parameters
    range                   = 1000:1019,
    postprocess             = true,
    gpu                     = true,
    Ncores                  = 20,
  )

Dependencies

Julia (5.1)

Libraries

Julia Packages

Copyright (c) 2018 Benjamin von Ardenne