UltraScan Version

Manual


SOMO HPLC-SAXS Module Options Module

Last updated: May 2014

SOMO HPLC-SAXS options

The first set of options deals with baseline removal tools. By deafult, the US-SOMO HPLC-SAXS module will utilize an Integral of I(t) baseline removal tool. The method is based upon the assumption that capillary fouling deposits are formed in proportion to the sample intensity while exposed to the beam (and that the buffer is not responsible). We have developed a mathematical model of this condition and implemented it as the integral baseline procedure. This is an iterative procedure and the number of steps can be set in the Maximum iterations: field (default: 5 iterations). As part of this procedure, the alpha value corresponds to the intensity fouling deposits constant and an early termination criteria can be defined here which will stop the iterative procedure when the difference in alpha between iterations is less than or equal to the alpha early termination limit field.
The program will generate a baseline at each iterative step. By selecting the Produce separate baseline curves checkbox, each baseline will be generated and can be shown in the graphics window. This could be helpful to check if the integral baseline tool has reached convergence. However, it should be deselected before applying the integral baseline tool to multiple files, to avoid the unnecessary generation of many baseline files.
For special needs or very minor baseline correction requirements, the original linear baseline implementation (Brookes et al., J. App. Cryst. 46:1823-1833, 2013) is available by selecting the Linear baseline removal checkbox. A description of the linear baseline removal tool can be found here)

The next set of options deals with the Gaussian mode available. Four alternative checkboxes are available:

In the Miscellaneous options section there is the option of saving the °.csv files in transposed format, by selecting the Save CSV transposed checkbox.

It is followed by the I(t) negative integral check window field, where the sliding window size for the negative integral test can be set (default: 25). As described previously, this is the size of a sliding window over adjacent frames. If the sum of I(t) values within the window is less than the negative of sum of the corresponding SD values, the I(t) curve will be identified and dropped during the Make I(t) and optionally dropped during the Test I(t) procedures.

The last line contains the checkbox for the On Make I(t), discard I(t) with no signal above std. dev. multiplied by: and its associated field (default: checked with 4 as the multiplier value). This tests whether or not there is any point in the I(t) curve where the I(t) value is greater than the SD of the point of I(t) multiplied by this field. If the test fails, the I(t) curve is assumed to contain no signal and is dropped with an appropriate messagebox.


www contact: Emre Brookes

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Last modified on May 19, 2014.