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Manual |
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:
where a0, a1, a2, and a3 are the area, center, width, and distorsion, respectively, of the half-Gaussian modified Gaussian(s).
where a0, a1, a2, and a3 are the area, center, width, and distorsion, respectively, of the exponentially modified Gaussian(s).
where a0, a1, a2, a3, and a4 are the area, center, width, distorsion 1, and distorsion 2, respectively, of the exponentially + half-Gaussian modified Gaussian(s).
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.
This document is part of the UltraScan Software Documentation
distribution.
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Last modified on May 19, 2014.