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Chi-Square Filter

Compares calculated scattering profiles to user supplied interpolated experimental scattering profiles.

Accessibility

The Chi-Square Filter module is accessible from the Analyze section of the main menu.

Basic Usage

The purpose of the module is create compare theoretical scattering profiles to interpolated experimental data.

Users supply an input data file containing three columns: q, I(q), and error of I(q) at each q-value. In addition, a value of I(0 usually obtained by Gunier analysis.

Notes

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Protein: Single Contrast

Screen Shots and Description of Input Fields

This example compares a set of scattering profiles to the interpolated experimental data obtained in 100% D2O buffer for K48 linked di-Ubiquitin. The scattering profiles were calculated using SasCalc.

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The expression syntax is simple, for example,

        x2 < 15
            

will set all frames that have a chi-square value less than 15.0 to 1.0 in the weight file, all other frames will be set to zero. You can link expressions together, and it is best to do so using parentheses to prevent errors,

        (rg < 19) and (x2 < 20)

will set frames with Rg values less than 19.0 and x2 values less than 20.0 equal to 1.0, otherwise they are set to zero.

One can not simultaneously select for both "rg" and "x2" in the same expression.

Example Output

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The output will show a plot of the interpolated data and scattering profiles from the best, worst, and average structures in the ensemble of scattering profiles.

Note that roll-over help will indicate options to resize, zoom and reset the view of the plot.

Results will be written to a new directory within the given "run name". For example, in the figure it is noted that the structures and dimensions were saved files within the current project directory within the chosen "run name" directory.

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./run_0/chi_square_filter/neutron_D2Op_100/bestworstfile.txt
./run_0/chi_square_filter/neutron_D2Op_100/averagefile.txt
./run_0/chi_square_filter/neutron_D2Op_100/x2file.txt
./run_0/chi_square_filter/neutron_D2Op_100/sas_spectra_plot.txt
./run_0/chi_square_filter/neutron_D2Op_100/x2_vs_rg_plot.txt
./run_0/chi_square_filter/neutron_D2Op_100/x2_lt_15.txt
./run_0/chi_square_filter/neutron_D2Op_100/x2_19_20.txt

The calculated scattering profiles normalized to the experimentally determined I(0) value are found in:
    ./run_0/chi_square_filter/neutron_D2Op_100/spectra
    

Visualization

None

Files Used and Created in Example

Protein-Deuterated Protein Complex: Multiple Contrasts

Screen Shots and Description of Input Fields: 0% D2O

This example compares a set of scattering profiles at two different contrasts to interpolated experimental data obtained in 0% and 85% D2O buffers for a protein complex consisting of two subunits: PAI (60% deuterated) and VN (protonated). VN has a long flexible tail. The scattering profiles were calculated using SasCalc.

First, the scattering profiles calculated for the complex in 0% D2O buffer are compared to the interpolated experimental data obtained in 0% D2O buffer.

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Example Output: 0% D2O

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The output will show a plot of the interpolated data and scattering profiles from the best, worst, and average structures in the ensemble of scattering profiles.

Note that roll-over help will indicate options to resize, zoom and reset the view of the plot.

Results will be written to a new directory within the given "run name". For example, in the figure it is noted that the structures and dimensions were saved files within the current project directory within the chosen "run name" directory.

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./run_0/chi_square_filter/neutron_D2Op_0/bestworstfile.txt
./run_0/chi_square_filter/neutron_D2Op_0/averagefile.txt
./run_0/chi_square_filter/neutron_D2Op_0/x2file.txt
./run_0/chi_square_filter/neutron_D2Op_0/sas_spectra_plot.txt
./run_0/chi_square_filter/neutron_D2Op_0/x2_vs_rg_plot.txt

The calculated scattering profiles normalized to the experimentally determined I(0) value are found in:
    ./run_0/chi_square_filter/neutron_D2Op_0/spectra
    

Screen Shots and Description of Input Fields: 85% D2O

Now, the scattering profiles calculated for the complex in 85% D2O buffer are compared to the interpolated experimental data obtained in 85% D2O buffer.

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Example Output: 85% D2O

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The output will show a plot of the interpolated data and scattering profiles from the best, worst, and average structures in the ensemble of scattering profiles.

Note that roll-over help will indicate options to resize, zoom and reset the view of the plot.

Results will be written to a new directory within the given "run name". For example, in the figure it is noted that the structures and dimensions were saved files within the current project directory within the chosen "run name" directory.

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./run_0/chi_square_filter/neutron_D2Op_85/bestworstfile.txt
./run_0/chi_square_filter/neutron_D2Op_85/averagefile.txt
./run_0/chi_square_filter/neutron_D2Op_85/x2file.txt
./run_0/chi_square_filter/neutron_D2Op_85/sas_spectra_plot.txt
./run_0/chi_square_filter/neutron_D2Op_85/x2_vs_rg_plot.txt

The calculated scattering profiles normalized to the experimentally determined I(0) value are found in:
    ./run_0/chi_square_filter/neutron_D2Op_85/spectra
    

Note that the directory structure has been preserved and that there are now two directories under ./run_0/chi_square_filter. If the advanced input box had not been checked, the entire chi_square_filter directory would have been overwritten and the neutron_D2Op_0 directory would have been deleted.

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Visualization

In this example, the calculated scattering profiles for the complex in 85% D2O buffer, where the deuterated PAI subunit is nearly contrast matched, sometimes have a zero or slightly positive slope at low q values when plotted as ln(I(q)) vs q^2 (Guinier) curves . Thus, Rg is not defined in these cases. The Rg values are listed as "nan" in the x2_vs_rg_plot.txt and x2file.txt files. Also note that the Rg values vary widely in 85% D2O buffer since the long flexible linker of the VN component covers a wide range of conformation space and there is almost no contribution from the deuterated PAI subunit. The Rg values don't vary quite as much in 0% D2O buffer due to the substantial contribution of the deuterated PAI subunit.

The results can be downloaded using the links below. Download the zip file to examine the calculated scattering profiles in the /spectra folders.

Files Used and Created in Example

Limitations

Simple comparison is done between theoretical and experimental data.

Reference(s) and Citations

  1. Numerical Recipes: The Art of Scientific Computing (3rd ed.) W. H. Press, S. A. Teukolsky, W. T. Vetterling, B. P. Flannery, New York: Cambridge University Press. ISBN 978-0-521-88068-8 (2007). BIBTeX, EndNote, Plain Text

  2. SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints J. E. Curtis, S. Raghunandan, H. Nanda, S. Krueger, Comp. Phys. Comm. 183, 382-389 (2012). BIBTeX, EndNote, Plain Text

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