Input Files

Parameter File :

All the parameters are given in this file.

sample.inp :

# This is a sample input file for

# FRETsg v1.0

sample.pos

Positions

sample.dis Distances

sample.pdb

Output PDB-File

Number of Configurations to create (max. 2000)

0.05

Gradient Threshold of Minimization ( 0.0 - 1.0 )

FALSE

Fluctuation Analysis [TRUE/FALSE]

Number of (accepted) MC Steps (max. 10000)

FALSE

Write Mirror Structure [TRUE/FALSE]

TRUE

Write PovRay Input [TRUE/FALSE]

No Configurations: The number of configurations created. Each configuration is created by a minimization that starts from a random configuration. This is done to find all (maybe different) configurations that obey the given distance constraints.

Gradient Threshold: The smaller this value, the better is the minimized model, but the more time consuming is the calculation. (recommended: 0.005).

Fluctuation Analysis: The Fluctuation Analysis performs a Monte-Carlo Simulation to create an ensemble, that is defined by the given standard deviation of the distances in the Distances File (*.dis).

MC Steps: The Number of accepted Monte-Carlo steps. (recommended: 50).

Mirror Structure: The handedness of the model is chosen by chance. The mirrored structure is of course also a possible solution.

Povray Input: Writes a Povray Input file.

Positions File :

All the labels must be declared here. This therefore defines the number of positions you want to calculate. Comment lines are defined by a leading "#" character, like in all input files.

sample.pos :

# This is a sample positions file

# for FRETsg v1.0

# known fit X Y Z

#Label [ only if known=1 ]

10 1 1 3.0 4.0 5.0

20 1 1 5.0 1.0 10.0

30 0 1 -3.4 5.4 21.0

40 0 1

50 0 0

Column:

#1 Label: All the labels from the DistancesFile (*.dis) have to be defined here. A label must be positive integer.

#2 Known-Flag: If the position of a label is known, then also the distances between all known labels are known. FRETsg uses all distances between known labels, even if they are not given in the DistancesFile (*.dis). But if a distance between two known labels is defined in the DistancesFile (*.dis), then the distance calculation from the given positions is ignored. If the flag is set to 1, then all three coordinates must be given; if set to 0, the coordinates are ignored and can also be left blank.

#3 Fit-Flag: Labels with fit-flag set to 1 are used for fitting all configurations to the first configuration. The choice of labels used for fitting usually affects the interpretation of the result, so one should try to use different settings to get a feeling for the model.

#4 X-Coordinate: Only necessary if Known-Flag = 1

#5 Y-Coordinate: Only necessary if Known-Flag = 1

#6 Z-Coordinate: Only necessary if Known-Flag = 1

Distances File

Here the distance are given between Label1 and Label2.

sample.dis :

# This is a sample Distances File

# for FRETsg 1.0

#Label1 Label2 Distance Width

10 20 10.0 1.0

10 30 10.0 1.0

20 30 10.0 1.0

10 40 25.0 1.0

20 40 25.0 1.0

30 40 25.0 1.0

10 50 40.0 1.0

20 50 40.0 1.0

30 50 40.0 1.0

Column:

#1 Label1 (must be defined in Positions File (*.inp) )

#2 Label2 (must be defined in Positions File (*.inp) )

#3 Distance between Label1 and Label2 (in arbitrary units)

#4 Standard deviation of the distance (error or/and fluctuation)