UltraScan Version

Manual


Indirect Fourier Transform (IFT) Module:

Last updated: January 2018

Synopsis

The Indirect Fourier Transform (IFT) Module transforms experimental I(q) curves to produce the pairwise distance distribution histogram P(r) curve using Bayesian Analysis. This module is an interface to BayesApp of Steen Hansen (J. Appl. Cryst. (2000). 33, 1415-1421; J. Appl. Cryst. (2008) 41, 436-445; J. Appl. Cryst. (2012). 45, 566-567; J. Appl. Cryst. (2014). 47, 1469-1471) The method of Glatter (Glatter, O. (1977). J. Appl. Cryst. 10), requires prior estimates of Dmax and a regularization parameter. Steen introduced methods to determine these parameters automatically using Bayesian Analysis methods. Further details about the program can be found in the above references.

Details

The IFT module can be run by simply pressing the IFT button after loading an experimental SAXS curve into the SOMO-SAS Simulation module.

SOMO-SAS window with one experimental curve loaded

Note that this method requires that the SAS curve contains a full set of experimental errors. If none are loaded, a messagebox will appear stating this.

If you have multiple SAS curves loaded with experimental errors, a window will appear asking you to choose which one to process:

IFT window file chooser

After pressing the IFT button, the IFT window will appear:

IFT parameters

No data entry is required. You can simply press the "Process" button to begin the IFT run. Alternatively, you can specify any or all of the following information:

Additional information about these fields may be found in the references.

The following buttons are available at the bottom of the window:

After pressing Process, the progress will be displayed in the text area:

IFT process

When processing is complete, three files are created, and you may be asked about overwriting them if duplicately named files already exist. Additionally, for the P(r) curve to display, a molecular weight needs to be known for scaling. The first time a curve is processed, a window will appear:

IFT process mw

Where you can enter the molecular weight. This is used for scaling of the P(r) curve and if you do not have a molecular weight, you can click "Do not normalize". If you have previously loaded a PDB into the main SOMO window during the session, or entered a molecular weight for a differently named curve, you can select it from "Previously recorded MWs".

After processing, the three files created are: the original_file_name_summary.txt containing the summary information including Rg, axial ratio, chi^2 and Dmax, original_file_name_ift.sprr containing the P(r) final curve data and the original_file_name_fit.ssaxs file which is the smoothed I(q) curve back-computed from the P(r). The P(r) and smoothed I(q) curves will be displayed, for example (with Legends and error bars on):

IFT results

Additionally, a window showing the residuals between the smoothed I(q) curve and the experimental data will be shown:

IFT residuals

Looking more closely at the output:

IFT process textarea

The dark red text is from the direct output of the program. Details of the progress are written during the run, including values of some parameters and the chi-square fit of the back-generated I(q) to the experimental data. There occasionally may be IEEE errors in red, this is generally ok and typically happens for values of parameters that produce bad solutions during the search. After "IFT finished" in black, appear the summary data, including a note about "Convergence of algorithm":

IFT process textarea convergence

It should read "OK" or at least "almost OK". If it is "NOT OK", then you could try fewer Number of points p(r) and/or provide estimates of Maximum diameter and/or Starting value for the Lagrange multiplier (Alpha).

Additional information including the values and standard deviations for the parameters follows the "Convergence of algorithm" message.

After summary information, the original_file_name_ift.sprr and original_file_name_fit.ssaxs files are loaded, and the normal details of loading a file are written. The P(r) produced generally does not have uniform grid spacing, so it will be rebinned for display, but the written file will retain the original r-grid. Finally, the files created with their full paths are shown. These files are now available for general usage within the SOMO-SAS Simulation module.




www contact: Emre Brookes

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Last modified on January 10, 2018.