Transition density coordinates files

Transition density coordinates files are ASCII files with the extension .txt. They are usually found in the main/transition_analysis/clustering folder.

Table of contents

  1. File name
  2. Structure

The Transition density coordinates files are written in an ASCII format and contains the settings used to build the TDP and the resulting 3D-coordinates.

They are created in the /transition_analysis/clustering analysis sub-folder after exporting ASCII coordinates (x,y,occurrence) from widow 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 and is appended with the extension _[Ddd]_coord, where [Ddd] is the data type written in the file.

Data types supported in transition density coordinates 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]

The extension _[Ttt] is added to the data type [Ddd] if a particular subgroup of molecules is analyzed, with [Ttt] the corresponding molecule tag.

Structure

TDP settings and 3D-coordinates are written using the following structure:

TDP settings

TDP settings include the type of count used to sort transitions into bins, as well as axis labels, limits and bin sizes. Settings are written in the first line of the file such as:

one transition count per molecule: [...]
x-axis: value before transition (m)
y-axis: value after transition (m*)
z-axis: occurence of transition amp(m,m*)
x-lim: [...,...], x bin:  [...]
y-lim: [...,...], y bin:  [...]

3D-coordinates

TDP 3D-coordinates are organized column-wise such as:

  • columns before trans. and after trans. containing respectively the x- and y-axis of the TDP
  • column occurence containing the z-values of the TDP
before trans.	after trans.	occurence
-1.950000e-01	-1.950000e-01	0
-1.950000e-01	-1.850000e-01	0
-1.950000e-01	-1.750000e-01	0