Kinetic model files

Kinetic model files are ASCII files with the extension .txt. They are usually found in the main/transition-analysis/kinetic model analysis folder.

Table of contents

  1. Description
  2. File name
  3. Structure

Description

Kinetic model files are data-specific and contain parameters of the kinetic model inferred in Transition analysis.

They are created in the /transition_analysis/kinetic-model analysis sub-folder when exporting results in window Export options of module Transition analysis.

File name

The file is named by the user during the export process. By default, the file is named after the selected project file.

The file name is appended with the extension _[Ddd]_mdl where [Ddd] is the data type written in the file.

Data types supported in dwell time files are:

  • I[i]-[L]: intensities in detection channel indexed [i] upon illumination with laser wavelength [L] nm
  • FRET[D]to[A]: FRET from donor emitter detected in channel indexed [D] to acceptor emitter detected in channel indexed [A]
  • S[D]to[A]: stoichiometry associated to donor emitter detected in channel indexed [D] and acceptor emitter detected in channel indexed [A]

Structure

The parameters of the inferred kinetic model are organized column-wise with:

  • column states containing state indexes
  • column values containing state values
  • column lifetimes(s) containing the state lifetimes calculated as the inverse sum of the exit rate coefficients
  • column initial prob. containing the state initial probabilities
  • columns k(s-1) containing the matrix of transition rate coefficients where row numbers correspond to the state index before transition and column numbers to the state after transition
  • columns +dk(s-1) and -dk(s-1) containing the positive and negative errors of transition rate coefficients calculated as described in Transition analysis Workflow
states	values	lifetimes(s)	initial prob.	k(s-1)	k(s-1)	k(s-1)	+dk(s-1)	+dk(s-1)	+dk(s-1)	-dk(s-1)	-dk(s-1)	-dk(s-1)
1	-4.998780e-03	5.185646e+01	2.203390e-01	0	1.153360e-03	1.813064e-02	0	7.295450e-04	8.949940e-04	0	4.070347e-03	4.304173e-04
2	6.950000e-01	4.314437e+01	7.568592e-01	1.255807e-04	0	2.305242e-02	2.205439e-04	0	1.801500e-03	9.300039e-03	0	9.665214e-04
3	6.950000e-01	2.398177e+00	2.280182e-02	1.288703e-01	2.881131e-01	0	2.317237e-02	5.438044e-02	0	1.878421e-02	4.398762e-02	0