Frequently asked questions — Irena¶
This section collects questions that have been asked by users over time, typically by email, where the answers are of general interest. There is no specific ordering; searching this page for a keyword is the most efficient way to find a relevant answer.
List of subjects¶
FAQs¶
Citation¶
Jan Ilavsky and Peter R. Jemian, “Irena: tool suite for modeling and analysis of small-angle scattering”, Journal of Applied Crystallography, vol. 42 (2009).
Do modeling populations have a required order?¶
The Unified Fit tool requires a specific ordering of levels — level 1 must correspond to the smallest features, level 2 to the next larger, and so on. This can be challenging when a new structural level appears partway through processing a series of samples. Does the Modeling package have a similar ordering requirement?
The answer is no. Modeling populations can be arranged in any order. A recommended approach is to assign population 1 to the dominant scattering component and add further populations as needed. Because there is no required ordering, Modeling cannot offer some of the conveniences of Unified Fit (such as automatic RgCO linking), and careful tracking of what each population represents is essential. The “What is this” field for each population is strongly recommended for this purpose.
What do I do if I need a different Form Factor?¶
If the form factor you need is not included in Irena, you can write your own function. Alternatively, you can adapt form factors or structure factors from the NIST Igor data analysis package. Contact the developer for assistance — particularly if the form factor is already implemented in the NIST package. More details are available here.
Why does Modeling warn against using multiple Unified levels?¶
Unified Fit requires a specific level ordering (see above) which enables the code to perform internal consistency checks and to automatically link the RgCO parameter between adjacent levels (see below). Neither of these capabilities is available in the Modeling tool. It is therefore strongly recommended to use the Unified Fit tool when multiple Unified levels are needed — not the Modeling tool, as this is more complex and more prone to error.
For systems where Unified Fit is not sufficient (e.g., a combination of Unified levels with size distributions or diffraction peaks), multiple Unified levels in the Modeling tool can be used, but extra care is required.
What is RgCo in Unified Fit and why does it matter?¶
RgCO is a critical parameter in Unified Fit that is frequently misunderstood. Incorrect use leads to physically meaningless fits.
Many structures studied by small-angle scattering scatter at multiple length scales simultaneously — even a simple cylinder with aspect ratio > 1 has two distinct length scales (radius and length), each producing a Guinier-like feature with its own Rg. See Cylinder form factor.
To model such a system in Unified Fit, two levels are used. Level 1 fits the smaller dimension (e.g., radius at high Q) and Level 2 fits the larger dimension (e.g., length at low Q), including the power-law slope between the two Guinier regions (approximately −1 for a cylinder). However, the power law of Level 2 will eventually exceed the measured scattering data at high Q.
To merge the two levels into a single physically meaningful representation of one population of scatterers, the RgCO parameter of Level 2 must be set equal to the Rg value of Level 1. Unified Fit provides a checkbox to link RgCO of level n to the Rg of level n−1 automatically.
The same principle applies to systems with more than two length scales. See also: Do Modeling populations have a required order?
How does Irena obtain absolute volume fractions and specific surface areas?¶
Irena expects properly calibrated input data:
The Q vector must be calibrated in units of Å-1.
For absolute volume fractions or specific surface areas, the intensity must be on absolute scale in units of cm2/(cm3·sr), commonly written as cm2/cm3 or cm-1.
When absolute intensity data are provided and the correct scattering contrast is entered, Irena outputs correct volume fractions.
For absolute calibration using Glassy Carbon SRM 3600, see:
Allen, A. J., Zhang, F., Kline, R. J., Guthrie, W. F., and Ilavsky, J. “NIST Standard Reference Material 3600: Absolute Intensity Calibration Standard for Small-Angle X-Ray Scattering.” Journal of Applied Crystallography 50(2) (2017): 462–474. http://dx.doi.org/doi:10.1107/S1600576717001972
A video tutorial on absolute calibration is available on the Irena YouTube channel: https://www.youtube.com/watch?v=FM5w2hwT7Ns
Irena expects input data that are fully corrected for sample thickness and all instrument effects. If needed, refer to the Nika section of this manual.