Command line options


FretTrace receives

all input parameters from the command line, so it can easily be used within

shell-scripts. Available options are:


 frettrace [-R radius] [-min min_distance] [-max max_distance]


[-d #distance_bins] [-t #time_bins | -dt time_increment]


[-D diff_coeff | -Dmin min_coeff -Dmax max_coeff -n #runs]


infile [-s] [-eps] [outfile] [-xmgr] [traj-file]




-R radius

Förster radius [nm] (default: 6.5).

This is the distance, where the donor and acceptor intensities are equal.

It depends on the dyes which are used in the experiment.

-min min_distance

Specifies the smallest distance plotted

in the distance distribution map [nm] (default: 0.0)

-max  max_distance

Specifies largest distance plotted in the distance distribution map [nm] (default: 2*radius). The smaller the distance

distribution range at a given number

of grid points, the higher the distance resolution. Attention: The range

( [

min_distance,max_distance] ) should not be too small, due to

possible edge effects. The distance distribution should be near zero at the

edges of the distance range.

-d  #distance_bins

Number of grid points for distance axis

(default: 400).

-t  #time_bins

Number of grid points for time axis (default:

1000). Another way of defining the time axis resolution is the 



-dt  time_increment

Grid resolution for time axis [mu s].

Alternative to

-t for defining the number of grid points

of the time axis.

-D  diff_coeff

Diffusion coefficient [1e-14 m^2/s] (default:

1.0) of the distance fluctuations. To find the most probable value, use the


-Dmin-Dmax and -n instead. From the calculated likelihood

function one can read the corresponding D-value of the maximum.

-Dmin  min_coeff

Minimum diffusion coefficient [1e-14 m^2/s]

(default: 0.01). Only used in the calculation of the likelihood function

for each D-value between 

min_coeff and max_coeff.

-Dmax  max_coeff

Maximum diffusion coefficient [1e-14 m^2/s]

(default: 100.0)

-n  #runs

Output likelihood for #runs different diffusion

coefficients in the range [



Input file for photon arrival times 

(see file format description)


Output file for distance distribution map

or likelihood function for different diffusion coefficients. (see file format

description of

  distance distribution map or of likelihood of diffusion values ).   


Write distance distribution in short format

for pictures  (see file format description)


Write distance distribution to encapsulated

postscript file


If given, write average trajectory and

deviation to traj-file   (see file format



Write trajectory in xmgr-format



If -D is given (default),

only one run is performed,


and a distance distribution map is written to outfile.

If -Dmin and -Dmax

are given, #runs runs are performed,


and the likelihood for each D-value is written to outfile.


File Formats
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