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FretTrace 1.0

Helmut Grubmüller and Gunnar F. Schröder

Overview


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. 


FretTrace
  • 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.

Reference


G. F. Schroder and H. Grubmuller, J. Chem. Phys. 119: 9920-9924 (2003) (download paper)

Downloads:

linkPfeil C Source Code [11 KB]
linkPfeil Sample data set (optionally) [name: burst.dat !] [14 KB]
linkPfeil Windows / DOS binary [246 KB]

Installation


Unix/Linux

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


Windows

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

 

Test

frettrace-data.zip 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
    \/          www.mpibpc.mpg.de/groups/grubmueller/start/people/hgrub ; hgrubmu@gwdg.de
               Reference: G. Schroder and H. Grubmuller (submitted)
 

  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: burst.out
  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.





linkPfeil Command line options, Parameters, File Formats
linkPfeil FretTrace is Free Software Available Under the GNU GPL
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© 2012, Max Planck Institute for Biophysical Chemistry, Göttingen