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