DynaFit Scripting Manual

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Progress Curves

Experimental data are identified in the script file in one of three sections:

• [progress] : time course of (bio)chemical reactions
• [velocities] : initial reaction velocities
• [equilibria] : equilibrium binding data.

In this chapter we discuss the design of the [progress] section of the script file. The [progress] section in each script file must contain the following keyword:

• file : identifies the datafile to be simulated or fitted
• mesh : must be present in all progress curve simulations (but not in data fitting); this keyword identifies the mesh of output points (independent variable) for the simulator.

Optionally, the [progress] section can contain the following keywords:

• local : requests local analysis of the experimental data (each progress curve is analyzed separately);
• directory : file directory in which data files are located;
• extension : datafile extension (must be the same for all datasets);
• error : if the measurement errors are known, the nature of the error function (relating standard error of each measurement to the magnitude of the measured quantity) the can be defined here;
• offset : a value to be subtracted from a progress curve on the signal axis (e.g., ``baseline'' absorbance);
• delay : a value to be added to a progress curve on the time axis (mixing delay time);
• concentration : concentrations of reactants specific to the given dataset;
• responses : molar response coefficients specific to the given dataset;
• equilibrate / dilute : for kinetic experiments that are preceded by the equilibration of reactants;

The primary function of the [progress] section is to give the location of the experimental or simulated progress curve files. Several preliminary examples are given below.

Example 1

[progress]
   offset = 0
   file ./examples/reductase/data/i0.txt

Example 2

[progress]
   directory    ./examples/conotoxin/data
   extension    txt
   files            058s1, 058s2, 024s,  105s, 115s, 186s
   vary conc.   L = 0.586, 0.586, 0.244, 1.05, 1.15, 1.86

Example 3

[progress]
    local
    directory      ./examples/pepsin/data
    extension      txt
    offset         auto ?
    error          constant 0.00025 ; spectrometer noise
    delay          5
    files             1,  2,  3,  6,  7,  8,  9, 10, 11
    vary conc. I =    0,  0,  0,  1,  1,  1,  2,  2,  2
    files            14, 15, 16, 17, 18, 19, 23, 24, 25
    vary conc. I =  0.1,0.1,0.1,0.2,0.2,0.2,0.3,0.3,0.3

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Petr Kuzmic | Jul 12 2005