UltraScan Version

Manual


SOMO - Model Classifier Module:

Last updated: March 2012

SOMO Model Classifier Main

In this module you will find a tool for selecting a best matching model among a series of models, by comparing their pre-calculated hydrodynamic parameters with user-provided experimental values.

Model Classifier parameters settings
In the first panel, the experimental parameters to be used are entered, and the methods used to screen the computed results against them are set.

The currently available parameters are listed in the Select to enable variable comparison column, and include:

  • Sedimentation coefficient s [S]
  • Traslational diffusion coefficient D [cm^2/sec]
  • Stokes radius [nm]
  • Frictional ratio
  • Radius of gyration [nm] (from bead model)
  • Relaxation Time tau(h) [ns]
  • Intrinsic viscosity [cm^3/g]

Select the parameters you wish to use by clicking on their respective checkboxes.

Enter then the experimental values in the relative fields in the second column, Experimental value. Be careful to use the appropriate units, as indicated after each parameter in the first column.

The results can be sorted using several alternative criteria, listed under the Sort results group:

  • Using percentage difference subgroup:
    • By ranked % absolute difference This is the simplest procedure. Click on its checkbox to activate it, and rank the parameters according to a descending order (i.e. 1=most relevant) in the Rank field(s).

    • By weighted sum of % absolute differences This is a way to rank over multiple parameters without specifically assigning a numerical rank to each parameter. This is accomplished by computing a weighted sum of absolute differences of every included parameter. The weights do not have to add up to 1. Experimental values with higher confidence should be assigned higher weights. Click on its checkbox to activate it, select the parameters to be included in the Included column, and assigning a weight to each one in the Weight column.

  • Equivalence class controls subgroup:
    • By equivalence class rank Equivalence classes partition a range of values. A value that falls into a specific equivalence class is equivalent to all other values within the equivalence class. The range runs from the Minimun model value to the Maximum model value and is composed of Number of partitions equivalence classes. The equivalence class that contains the experimental value is given a distance of zero. Equivalence classes next to the one containing the experimental value are given a distance of 1, and so on. Adding up the distances of each of the selected variables gives the equivalence class rank. Click on its checkbox to activate it, and fill up the Number of partitions, Minimum model value and Maximum model value fields for each parameter.

The current parameters and the criteria used for the sorting can be saved in a file (extension *.smp) by clicking on the Save Parameters button. Reset Parameters will clear all fields. Previously saved parameters can be re-loaded by clicking on the Load Parameters button.

The Model classifier will write the results in a file. Under the Add columns to results header you will find three columns containing checkboxes, Experimental value, % Difference and % Absolute difference. Selecting one or more checkboxes will add the corresponding value(s) to the output file.

Model Clasifier csv processing

In the second panel, the calculated parameters are uploaded. They should be in *.csv files, most easily generated using the Save parameters to a file checkbox (and the Select Parameters to be Saved module) in the Hydrodynamic calculations section of the main US-SOMO window. Only the parameters present in the *.csv files, identified through their headers, will be then available in the Select to enable variable comparison column.

Pressing the Load button will open the filesystem dialog and allow importing the required *.csv files into the left-side window. Files can then be selected by clicking on each filename, which will transfer them to the right-side window, or by pressing the Select all button.
Remove will remove files from the list.
View will bring up the results of the classifier (see below).
Merge will join the selected files from the list into one csv file.
Set min/max will set the Minimum model value and Maximum model value from the values found in the selected files

The files listed in the right-side window can be then selected for processing by individually clicking on them, or by pressing the Select all button.
Remove will remove files from the list.
Merge will join the selected files from the list into one csv file.
Set min/max will set the Minimum model value and Maximum model value from the values found in the selected files

Once files has been selected, the Model Classifier can be launched by pressing the Process button, and the progress window at the far right will be updated. At the end, pressing View will open a window with all the selected columns:

Model Classifier view results

In the example above, the classifier used the weighted sum of % absolute differences to rank the models. By clicking on each column, the results can be sorted according to that column's values.

By pressing the Save button, a filesystem dialog will open allowing to save the results in a new *.csv file, which can then be opened with a standard spreadsheet. A typical results file after ranking by % absolute difference can be seen below:

Model Classifier csv results

www contact: Emre Brookes

This document is part of the UltraScan Software Documentation distribution.
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The latest version of this document can always be found at:

http://somo.uthscsa.edu

Last modified on March 16, 2012.