Trace file from simulation

Trace files from simulation are ASCII files with the extension .txt. They are usually found in the main/simulations/traces_ASCII analysis folder.

Table of contents

  1. Description
  2. File name
  3. Structure
  4. Compatibility

Description

These trace files are the simulated data of individual molecules written in ASCII format. They contain the molecule coordinates in the video, the simulated intensity- and FRET-time traces as well as the corresponding state trajectories.

They are created in the /simulations/traces_ASCII analysis sub-folder after exporting ASCII traces in panel Export options of module Simulation.

File name

The file is named by the user during the export process, and is appended with the extension _molMofN, where M is the index of the molecule written in the file and N the total number of simulated molecules.

Structure

The molecule coordinates in each video channel are written in the first file line such as:

coordinates 	xxx,yyy	XXX,YYY

with xxx,yyy and XXX,YYY, the x- and y-coordinates in donor and acceptor channel respectively.

Simulate time traces and state trajectories are organized column-wise with:

  • column time(s) containing time data in second
  • column frame containing frame indexes
  • columns Idon noise(a.u.) and Iacc noise(a.u.) containing donor and acceptor intensity-time traces respectively, in image or photon counts
  • columns Idon ideal(a.u.) and Iacc ideal(a.u.) containing the noiseless, background-free and gamma factor-free photon count-time traces of donor and acceptor respectively
  • column FRET containing FRET-time traces
  • column FRET ideal (blurr) containing noiseless, background-free and gamma factor-free FRET-time traces with camera blurring effect
  • column FRET ideal containing noiseless, background-free and gamma factor-free FRET-time traces without camera blurring effect
  • column state sequence containing state indexes
time(s)	frame	Idon noise(photons)	Iacc noise(photons)	Idon ideal(photons)	Iacc ideal(photons)	FRET	FRET ideal (blurr)	FRET ideal	state sequence
2.000000e-01	1	1.996415e+01	4.003952e+01	1.680000e+01	3.920000e+01	6.672846e-01	7.000000e-01	7.000000e-01	2
4.000000e-01	2	1.767607e+01	4.298884e+01	1.680000e+01	3.920000e+01	7.086278e-01	7.000000e-01	7.000000e-01	2
6.000000e-01	3	1.528009e+01	3.938020e+01	1.680000e+01	3.920000e+01	7.204535e-01	7.000000e-01	7.000000e-01	2

Compatibility

Simulated trace files can be imported in modules Trace processing and Transition analysis for analysis by adjusting the Import options to the actual file structure.