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cryoem-data-simulation

Python3 tools for simulating cryoEM particle data, analyzing alignments, perturbing data, and more.

Built with help from https://github.com/mbrubake/cryoem-cvpr2015 and https://github.com/asarnow/pyem.

Features

Data Simulation

  • simulate_particles.py: Core script for multithreaded simulation of cryoEM particle stacks.
  • simulate_dual_stacks.py: Simulate two stacks from two different volumes but match noise, ctf, and projection angle per particle between the stacks.
  • simulate_dual_stacks_rv.py: Like simulate_dual_stacks but specify two sets of input volumes and probability weights (e.g. to model particle heterogeneity or classes).

Alignment Analysis

  • analyze_alignment.py: Given experimental alignment parameters (e.g. cisTEM .par file) and theoretical parameters (e.g. from simulate_dual_stacks.py) from two different reconstructions, compare the distributions of angular and positional errors.

Tellurification

  • tellurify.py: Replace methionines with telluromethionines or phenylalanines with tellurienylalanines in a PDB file.

Data Perturbation

  • perturb_alignment.py: Given a star file with some Euler angles, perturb these orientations by a characteristic overall angular error.

Simulating Data

Note: The pyx modules in cryoem-cython-pyx need to be compiled for your system. See below.

Simulate data

$ python3 simulate_particles.py <input_mrc_path> <output_directory> --n_particles n --snr s

Other Flags:

  • --snr: Specify a signal to noise ratio for the particles
  • --sigma_noise: Specify a numeric standard deviation for the noise to be added (will override --snr)
  • --cpus: Specify the number of processors to use (otherwise will use (n_cpus_available - 1)
  • --overwrite: Don't prompt user for confirmation if the output directory exists and will be overwritten
  • The microscope and CTF parameters can be changed in the params dict in main().

Inputs

  • input_mrc: mrc volume from which the volume data, pixel size, and box size will be read

Outputs (in output_directory)

  • simulated_particles.mrcs: mrcs particle stack containing the particle image data
  • simulated_particles.star: Relion star file describing the simulated particles
  • simulation_metadata.txt: Log of the simulation parameters and performance
  • plot.png: Visualization of the first 8 particles

plot example

To compile the pyx files (in cryoem-cython-pyx)

Compile using clang or gcc and then either move or symlink the .so files into the cryoem directory. For macOS

$ export C_INCLUDE_PATH=/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/Headers:/usr/local/lib/python3.7/site-packages/numpy/core/include

$ python3 setup.py build_ext --inplace

For Linux

$ export C_INCLUDE_PATH=/home/<username>/.local/lib/python3.7/site-packages/numpy/core/include

Symlink the compiled modules

$ cd cryoem
$ ln -s ../cryoem-cython-pyx <result_so_file> <symlink_name>

Dependencies

  • Python3
  • numpy
  • scipy
  • cython
  • pyfftw (optional, but creates significant speedup)
  • matplotlib