Command line options, Parameters, File Formats

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` option.
`-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 options `-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 [ `min_coeff`,`max_coeff`].
`infile`	Input file for photon arrival times (see file format description)
`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
`traj-file`	If given, write average trajectory and deviation to traj-file (see file format description)
`-xmgr`	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