Manual

Self-Association Equilibrium Simulator:

You start the Self-Association Equilibrium Simulator by clicking on "Self-Association Equilibrium" in the Simulation sub-menu of the main menu. The main Self-Association Simulator window will appear. This software assumes that you concentration values are in molar units. if you are using different concentration units, you need to convert your association constants to molar units first.

This program allows you to simulate the relative amounts of monomer, dimer and tetramer species present in a self-association equilibrium. When you set the logarithm of the corresponding equilibrium constant by clicking on the arrows of the counter widgets, the program will calculate the distribution of each species using a root-finding algorithm.
Clicking in the plot area will draw a vertical bar corresponding to the concentration at that position and display the relative amounts of each species in the corresponding label.

Clicking on the "Write Data to File" button will create an ASCII data file with the relative concentrations of each species over the concentration range from 1 x 10^-10 molar to 1 x 10² molar. The data points are logarithmically spaced. Click here for file format information.

Explanation of Buttons and Fields:

Help: Display this help file
Update Graphs: Recalculate current settings and display the graph
Save Data to File: Save the current distribution to an ASCII formatted file. The data is saved in your results directory in a file called Simulation-.dat. For details on file formats, check here.
Print Plot Window: Load the printer control panel for printing of plot graphics
Close: Close this window and exit the self-association module

Stoichiometries for a two component model - these fields allow you to enter any stoichiometry for your association equilibrium. Fractional values are allowed. If you invoked this routine from a fitting panel of the self-associating model fitter, the values are read-only and cannot be changed.

Equilibrium constants - Use the counter buttons to change the value of the equilibrium constant (in molar units). The values shown are listed as the natural log of the association constant. The 1/2/3 arrow buttons adjust the value in steps of powers of 10. If you invoked this routine from a fitting panel of the self-associating model fitter, the values are read-only and cannot be changed.

Equilibrium Model - This field identifies the associated model. By default this model is the user-defined monomer-n-mer-m-mer model. If you invoked this routine from a fitting panel of the self-associating model fitter, the model used in the fitting routine will be listed here.

Project Name: The project name is used to identify the associated project when invoked from the fitting panel of a fitting module, and used in the file naming of the result file when saved to disk.

Species Indicator - The species indicators list the percentage of concentration contributed by each species (monomer, n-mer, m-mer) to the total concentration. You can drag the mouse through the plot area and a white vertical bar will indicate the total concentration. The relative amount of each species will be listed in the species fields.

www contact: Borries Demeler

The latest version of this document can always be found at:

http://www.ultrascan.uthscsa.edu

Last modified on January 12, 2003.

	Help: Display this help file Update Graphs: Recalculate current settings and display the graph Save Data to File: Save the current distribution to an ASCII formatted file. The data is saved in your results directory in a file called Simulation-.dat. For details on file formats, check here. Print Plot Window: Load the printer control panel for printing of plot graphics Close: Close this window and exit the self-association module
	Stoichiometries for a two component model - these fields allow you to enter any stoichiometry for your association equilibrium. Fractional values are allowed. If you invoked this routine from a fitting panel of the self-associating model fitter, the values are read-only and cannot be changed.
	Equilibrium constants - Use the counter buttons to change the value of the equilibrium constant (in molar units). The values shown are listed as the natural log of the association constant. The 1/2/3 arrow buttons adjust the value in steps of powers of 10. If you invoked this routine from a fitting panel of the self-associating model fitter, the values are read-only and cannot be changed.
	Equilibrium Model - This field identifies the associated model. By default this model is the user-defined monomer-n-mer-m-mer model. If you invoked this routine from a fitting panel of the self-associating model fitter, the model used in the fitting routine will be listed here. Project Name: The project name is used to identify the associated project when invoked from the fitting panel of a fitting module, and used in the file naming of the result file when saved to disk.
	Species Indicator - The species indicators list the percentage of concentration contributed by each species (monomer, n-mer, m-mer) to the total concentration. You can drag the mouse through the plot area and a white vertical bar will indicate the total concentration. The relative amount of each species will be listed in the species fields.