Introduction
Overview
This tutorial covers SAXS data processing with RAW. You will learn how to:
Process images into scattering profiles
Average, subtract and save scattering profiles
Find Rg and I(0) by Guinier analysis
Find molecular weight by six different methods
Do Kratky analysis and dimensionless Kratky analysis
Compare scattering profiles using residuals, ratios, and statistical tests
Load and process SEC-SAXS data
Carry out singular value decomposition (SVD) and evolving factor analysis (EFA) to evaluate and deconvolve SEC-SAXS data
Carry out regularized alternating least squares (REGALS) analysis to deconvolve SAXS data.
Do baseline correction on SEC-SAXS data
Merge SAXS/WAXS data from two detectors
Carry out Pair-distance distribution analysis (BIFT and GNOM)
Evaluate ambiguity of 3D shape reconstructions (AMBIMETER)
3D reconstructions with bead models (DAMMIF/N and DAMAVER)
3D reconstructions with electron density (DENSS)
Align 3D reconstructions with high resolution models (DENSS and CIFSUP)
Calculate theoretical scattering profiles from models and fit the theoretical scattering against experimental data (CRYSOL)
Save your analysis information and plots
Calibrate RAW for integrating images
Mask images for integration
Set up normalization and save processing settings
Set absolute scaling in RAW using water and glassy carbon
Set a molecular weight standard in RAW
Section 1 covers basic processing with RAW, and Section 2 covers advanced processing with RAW. Section 3 covers saving plots and plot data and opening data in other programs. Section 4 covers how to set up RAW for integrating images for those who do not already have a configuration file.
This tutorial is focused on how to use RAW, it is not necessarily a tutorial on best practices for SAXS data processing. The SAXS tutorial covers some basic processing and analysis best practices.
Requirements
BioXTAS RAW >= v2.2.0 (most recent is best).
Tutorial data.
Available from: https://sourceforge.net/projects/bioxtasraw/files/?source=navbar
ATSAS programs, >= v3.1.1 (for parts of Section 2 of the tutorial).
Download and installation instructions are available from: https://www.embl-hamburg.de/biosaxs/download.html
Requires a free registration for academic users. Proprietary users must pay to use.
Other useful materials
Video lectures from BioCAT’s Everything BioSAXS workshops, which can help you learn more about best practices for SAXS data processing.
Most tutorial sections have a linked video tutorial. A full playlist of the videos is available here:
ATSAS resources:
User forum: https://www.saxier.org/forum/
Electron density (DENSS) resources available at DENSS.org
Particularly useful is the section on visualizing the results and aligning with known structures.
Notes
If you are only interested in using RAW to process data, and are not interested in how to set up RAW to calibrate your data, you do not need to look at Section 4.
RAW depends on user feedback to get better. If you have questions, find bugs, or think a part of this tutorial is unclear, please let the developers know.
You can find additional developer contact information on the RAW website: https://sourceforge.net/projects/bioxtasraw/