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.
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.
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
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.