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
- Test the similarity of scattering profiles
- 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)
- Save your analysis information
- 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 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.
BioXTAS RAW >= v2.1.0 (most recent is best).
- Tutorial data.
- Available from: https://sourceforge.net/projects/bioxtasraw/files/?source=navbar
Other useful materials¶
Video lectures from BioCAT’s Everything BioSAXS workshops, which can help you learn more about best practices for SAXS data processing.
Each tutorial section has a linked video tutorial. A full playlist of the videos is available here:
Electron density (DENSS) resources available at DENSS.org
- Particularly useful is the section on visualizing the results and aligning with known structures.
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 3.
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/