HaMMy trace files

HaMMy trace files are ASCII files with the extension .dat. They are usually found in the main/video_processing/intensities/traces_HaMMy or main/traces_processing/traces_HaMMy analysis folder.

Table of contents

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

Description

These trace files are written in an ASCII format importable in the software HaMMy [1]. Each file contains intensity-time traces of a specific molecule and FRET pair, integrated from a single molecule video (SMV) or exported after trace processing.

They are created in the /video_processing/intensities/traces_HaMMy analysis sub-folder after creating and exporting HaMMy traces in panel Intensity integration of module Video processing, or in or /traces_processing/traces_HaMMy if exported from panel Sample managementof module Trace processing.

File name

The file is named by the user during the export process.

By default, the file is named after the video file loaded in Video processing or the project file in Trace processing from which data are exported, and is appended with an extension _mol[n]of[N]FRET[D]to[A]_HaMMy where [n] is the exported molecule index, [N] is the number of single molecules, and where [D] and [A] the channel indexes where donor and acceptor fluorescence are specifically detected.

Structure

FRET pair-specific intensity-time traces are organized row-wise by appending the same columns for each molecule, and column-wise with time data written in column 1, donor intensities in column 2 and acceptor intensities in column 3.

1.017500e-01	2067	1085
3.052500e-01	2013	1044
5.087500e-01	1950	1216
7.122500e-01	2405	1443

For consistency, intensity-time traces exported from module Video processing or Trace processing are always given as the sum of the brightest pixel intensities per video frame, regardless the units defined in Pixel intensity units or Intensity units respectively.

Compatibility

HaMMy trace files can be imported in external software HaMMy [1] and in MASH’s module Trace processing by adjusting the Import options to the actual file structure.

References

  1. S.A. McKinney, C. Joo, T. Ha Analysis of Single-Molecule FRET Trajectories Using Hidden Markov Modeling, Biophys. J. 2006, DOI: 10.1529/biophysj.106.082487