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Eros

A module that implements a heuristic algorithm using maximum entropy and simulated annealing to determine plausible sub-ensemble fits to scattering data.

Accessibility

The Eros module is accessible from the Alpha section of the main menu.

Basic Usage

The purpose of the module is to apply maximum entropy methods to explore viable combinations of scattering curves consistent with experimental data.

Users supply an input data file containing three columns: q, I(q), and error of I(q) at each q-value. A value of I(0), usually obtained by Gunier analysis, is required to normalize data. A path to a folder containing scattering data files, the number of files to use along with parameters to guide the fitting process.

Advanced options can be used in order to iterate the fitting process to evaluate the parameter space of the heuristic method as applied to your input data.

Upon completion, the module will make several plots in order to evaluate the quality of the maximum entropy fit(s).

Weight files are created that can be used by other modules to extract structures for further analysis.

Notes

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Single Trajectory

Screen Shots and Description of Input Fields

This example analyzes scattering profiles to interpolated experimental data using a set of fitting input parameters. The scattering profiles were calculated using SasCalc.

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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/eros/bestworstfile.txt

Visualization

None

Files Used and Created in Example

Limitations

Simple comparison is done between theoretical and experimental data.

Reference(s) and Citations

  1. SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions B. Rozycki, Y. C. Kim, G. Hummer, Structure 19, 109-116 (2011). BIBTeX, EndNote, Plain Text

  2. 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

  3. 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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