Welcome to ETSimulations’s documentation!

The ETSimulations package is designed to be a tool to the facilitate generation and processing of simulated cryo-electron tomography data.

• Raw tiltseries are generated with a combination of UCSF Chimera and the TEM-Simulator package. Simulated particles placed in the generated data can be based on either inputted PDB models or MRC files and manipulated with Chimera commands.

• Generated datasets are then available to be processed with any cryo-ET software; automatic processing options are available currently for the EMAN2 , IMOD, Dynamo, I3, and Artiatomi pipelines.

Table of Contents

• Installation
  • External dependencies
  • Setting up ETSimulations
• Simulation
  • Introduction
  • Simulation configuration parameters
  • Data set generation outputs
• Processing
  • Introduction
  • Available processors
    • The EMAN2 Processor
      • Parameters
        • steps_to_run
        • particle_coordinates_parameters
        • e2*_parameters objects
      • Running the generated script
    • The IMOD Processor
      • Reconstruction
      • Parameters
      • Using the IMOD Processor on real data
    • The Dynamo Processor
      • Required arguments
        • Using the Dynamo Processor on real data
          • Starting from IMOD
          • Starting from EMAN2
    • The I3 Processor
      • Parameters
      • Using the I3 Processor on real data
        • Starting from IMOD
        • Starting from EMAN2
    • The Artiatomi Processor
      • Introduction
        • A note on EMAN2
      • Parameters
        • General parameters
        • Artiatomi-specific parameters
        • Real data mode parameters
      • Further details by step
        • Reconstruction and Motivelist
        • Averaging
        • Refinement
      • Examples
• Guides
  • Simple simulations with the Basic Assembler
    • Introduction
    • Putting together the particle map
    • Setting up the simulation run
      • orientations_source
      • use_common_model
    • Running the simulation
    • The outputs
  • Particle assembly using Chimera
    • Useful commands
    • General tips
  • Simulating the T4SS
    • The T4SS Assembler
      • Custom configs
      • Metadata output
  • Making your own custom Assembler
    • What are Assemblers?
    • Setting up a new Assembler
    • The set_up_tiltseries function
      • Part 1
      • The __assemble_particle() function
      • Part 2
    • The reset_temp_dir and close functions
    • Conclusion
• Technical documentation
  • Software architecture
    • Simulation
      • Logging
      • Assemblers
  • Source code documentation
    • Primary Modules
      • ets_generate_data.py
      • ets_process_data.py
    • Simulation helper modules
      • Simulation
      • Chimera-related classes
        • Chimera Server
        • Chimera Command Set
      • Logging
    • Assembler modules
      • Basic Assembler
      • T4SS Assembler
        • The main Assembler class
    • Processor modules
      • EMAN2 Processor
        • EMAN2 Processor Template Script
      • IMOD Processor

Indices and tables

• Index

• Module Index

• Search Page