Command line options

FretTrace receives
all input parameters from the command line, so it can easily be used within shellscripts. 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] [trajfile]

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 topossible 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 dtoption. 
dt time_increment

Grid resolution for time axis [mu s].
Alternative to t for defining the number of grid pointsof the time axis. 
D diff_coeff

Diffusion coefficient [1e14 m^2/s] (default:
1.0) of the distance fluctuations. To find the most probable value, use the options Dmin, Dmax and n instead. From the calculated likelihoodfunction one can read the corresponding Dvalue of the maximum. 
Dmin min_coeff

Minimum diffusion coefficient [1e14 m^2/s]
(default: 0.01). Only used in the calculation of the likelihood function for each Dvalue between min_coeff and max_coeff. 
Dmax max_coeff

Maximum diffusion coefficient [1e14 m^2/s]
(default: 100.0) 
n #runs

Output likelihood for #runs different diffusion
coefficients in the range [ min_coeff,max_coeff]. 
infile

Input file for photon arrival times 
outfile

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 ). 
s

Write distance distribution in short format
for pictures (see file format description) 
eps

Write distance distribution to encapsulated
postscript file 
trajfile

If given, write average trajectory and
deviation to trajfile (see file format description) 
xmgr

Write trajectory in xmgrformat 

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 Dvalue is written to outfile.

File Formats 