FretTrace 1.0

Financial Support: Volkswagen Foundation Grant No. I/75 321

Single molecule Fluorescence Resonance Energy Transfer (FRET) experiments are a powerful and versatile tool for studying conformational motions of single biomolecules at a millisecond time scale. Typically, the small number of recorded photons limits the achieved time resolution. 


  • reconstructs nanometer distance trajectories from time-resolved single photon FRET recordings,
  • extracts the full information from the recorded photon arrival times,
  • provides rigorous error bounds and
  • is able to extract an effective diffusion coefficient for the distance fluctuations.

FretTrace is the implementation of a maximum likelihood based theory.


Schröder, G.; Grubmueller, H.: Maximum likelihood trajectories from single molecule fluorescence resonance energy transfer experiments. Journal of Chemical Physics 119 (18), pp. 9920 - 9924 (2003)




To install FretTrace, move the tar-file to your favourite directory and enter: tar xvzf frettrace-1.0.tar.gz

The source frettrace.c is just one ANSI-C-file without any system-specific stuff (except for malloc() --- RS6000 and NeXT users: pay attention!), so it should compile right away with something like cc -O2 -o frettrace frettrace.c -lm


Just unzip the zip-file into your favourite directory this will unpack the executable frettrace.

Test contains the file burst.dat.

To check your installation, type: frettrace burst.dat burst.out


The output should look like this:

 _      _    

FRETtrace 1.0   (C) 2002 Helmut Grubmüller, Gunnar Schröder

  \    / \   _    

Purpose: Create maximum likelihood trajectories

   \  /   \_/              

from single molecule FRET data



Reading photon arrival times from file burst.dat ... Done.

Read 230 photons (117 donor, 113 acceptor).

Start time: 7545472.000000 mu s   

End time: 7555268.500000 mu s   (Length: 9796.500000 mu s)

Output file for distance distribution map or likelihood:


Foerster radius: 6.5 nm

Smallest distance considered 0 nm (internal: -13 nm)

Largest  distance considered 13 nm (internal: 26 nm)

Number of grid points for time axis: 1000

Number of grid points for distance axis: 400 (internal:1200)

Will calculate distance distribution for diffusion coefficient D = 1e-14 m^2/s


Forward scan photons ...  100%  Done.

Backward scan photons ... 100%  Done.

Forward scan grid ...     100%  Done.

Backward scan grid ...    100%  Done.

Writing distance distribution P(r,t) to file burst.out ... Done.


FRETtrace ready. No errors.

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