Parameters

Parameter name	Description
PDB	Open PDB file. Only protonated files are read correctly. The naming scheme has to follow the “PARSE” convention of PDB2PQR
Sticky-Checkbox	If this checkbox is checked either the surface of the protein, as determined by the distance to the C-beta atoms, of the quenching amino acids are “sticky”. If this checkbox is unchecked the diffusion coefficient within the accessible volume of the dye is uniform.
Rs[A]	A radius (distance) below which parts of the AV are considered as “sticky”. If for instance the distance between these points of the AV and a C-beta atom is smaller than Rs the diffusion coefficient of these AV-points is multiplied by the “slow factor” (see below).
Slow factor	The diffusion coefficient of points within the AV which are closer than a critical distance to a stick object are multiplied by this scaling factor.
Label-Chain	Chain to which the dye is attached to
Residue	Residue to which the dye is attached to
Atom	Atom name of the dye attachment
Length	Linker-length in Angstroms of the dye
Width	Width of the dye-linker in Angstrom
Radius	Radius of the dye
dg	Grid spacing of the accessible volume
tau0	Fluorescence lifetime of the dye in absence of quenching
D	Diffusion coefficient of the dye when not sticking
Quencher	A list of quenching amino acids following 3-letter amino acid codes. The amino acids are separated by spaces
Quench radius	Distance below which the dye is quenched by an quenching amino acid
kQ	Rate constant of quenching
Exclude atoms	If this is checked the atoms with the names listed below are not considered as quenching atoms
Sim time	Length of the Brownian dynamics (BD) simulation
dt	Step length of the BD-simulation
nPhotons	Number of simulated photons
Frames	Resulting number of simulated frames
QY(F)	Simulated fluorescence quantum yield
collided	Fraction of dyes which collided with a quenching amino acid
nBins	Number of bins of the fluorescence intensity decay histogram
range	Range (in nanoseconds) of the fluorescence intensity decay histogram
skip	Number of frames which are skipped when BD-simulations are saved or visualized
Prefix	Prefix of AV-filenames when saved