Simulating the T4SS

Included in the ETSimulations repository are example files relating to the simulation of Type IV Secretion Systems. This tutorial covers the process of generating a data set from these as a way to demonstrate the simulation workflow. Rest of tutorial to be completed.

The T4SS Assembler

The T4SS Assembler class implements an Assembler to generate and modify fake particles using Chimera designed to approximate the structure of the Type IV Secretion System. It will create particles consisting of an inner

Custom configs

The parameters available for the T4SS Assembler through the YAML custom_configs are:

• membrane_pathstring

  The file path to the membrane segment MRC representing the inner membrane

• coord_errorobject with keys “mu” and “sigma”

  (Optional) Add Gaussian noise to the coordinates from the coord file. Random error values are sampled from a Gaussian distribution with mean “mu” and standard deviation “sigma” to be added to the each of x, y, z positions for the coordinates (in pixels). For example, using { “mu”: 0, “sigma”: 1 } as the value will result in a standard normal distribution being used for errors.

• orientations_tblstring

  A Dynamo orientations table which contains particle orientations found from a real data set, used to approximate the real-life particle orientation distribution

• orientations_errorobject with keys “mu” and “sigma”

  (Optional) Add Gaussian noise to the orientations samples from the orientations_table file. Random error values are sampled from a Gaussian distribution with mean “mu” and “sigma” standard deviation to be added to the Euler angles sampled for each particle. For example, using { “mu”: 0, “sigma”: 1 } as the value will result in a standard normal distribution being used for errors.

• rodstring

  The path to the MRC to use for the rods

• rootstring

  The path to the MRC to use for the central barrel

• num_rodsinteger

  The number of rods to place symmetrically around the central barrel

• rod_distance_from_centerfloat

  The distance (in Angstroms) away from the center of the barrel to place rods, i.e. the radius

Metadata output

Each stack simulated with the T4SS pipeline will produce the following metadata object within the sim_metadata.json file outputted.