Biological Small-Angle Neutron Scattering Workshop
Agenda:
Link to workshop agenda: https://conference.sns.gov/event/511/
Day 1: October 15, 2025
Teams Link: Join the meeting now
|
Schedule (EST) |
Activity |
Lead |
|
9:30-9:45 am |
Introductions |
Hugh O’Neill |
|
9:45-10:00 am |
Center for Structural Molecular Biology Overview |
Hugh O’Neill |
|
10:00-10:30 am |
Introduction to Small-Angle Neutron Scattering - Part 1 |
Volker Urban |
|
10:30-11:00 am |
Demonstration 1: Data reduction and background subtraction using SANS Super EASY |
Wellington Leite/ Sai Venkatesh Pingali/Alan Hicks |
|
11:00-11:15 am |
Break |
|
|
11:15-11:30 am |
Virtual tour of Bio-SANS |
Felicia Gilliland |
|
11:30-11:45 am |
Virtual Tour of Biology Laboratories |
Qiu Zhang |
|
11:44 am-12:45 pm |
Lunch |
|
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12:45-1:15 pm |
Introduction to Small-Angle Neutron Scattering -Part 2 |
Volker Urban |
|
1:15-1:45 pm |
Demonstration 2: Kratky plot, Guinier analysis, and Interparticle interferences |
Wellington Leite/ Sai Venkatesh Pingali/Alan Hicks |
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1:45 -2:00 pm |
Break |
|
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2:00-2:30 pm |
Demonstration 3: P(r) analysis |
Wellington Leite/ Sai Venkatesh Pingali/Alan Hicks |
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2:30-3:15 pm |
Experiment Set-up and Data Acquisition |
Sai Venkatesh Pingali |
|
3:15-4:15 pm |
Attendee Lightning Talks |
Hugh O’Neill |
Day 2: October 16, 2025
Teams Link: Join the meeting now
|
Schedule (EST) |
Activity |
Lead |
|
9:30-11:00 am |
Breakout and hands-on Session 1.0: Data analysis for solution scattering of biomacromolecular complexes Breakout and hands-on Session 2.0: Data analysis for hierarchical biosystems |
Wellington Leite/ Sai Venkatesh Pingali/Alan Hicks |
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11:00-11:15 am |
Break |
|
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11:15 am-12:00 pm |
Sample Preparation and Experiment Planning |
Wellington Leite |
|
12:00-1:00 pm |
Lunch |
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|
1:00 - 1:20 am |
Bio- and chemical deuteration |
Kevin Weiss/ Honghai Zhang |
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1:20-2:20 pm |
Breakout and hands-on Session 1.1: Data analysis for solution scattering of biomacromolecular complexes Breakout and hands-on Session 2.1: Data analysis for hierarchical biosystems (Free discussion)
|
Wellington Leite/ Sai Venkatesh Pingali/Alan Hicks |
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2:20-2:30 pm |
Break |
|
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2:30-3:00 pm
|
Q&A and Closing Remarks |
Wellington Leite |
Software required for Session 1
|
Software |
Source |
Application |
|
|
|
|
|
SANS Super EASY |
Installation guide |
Software developed at ORNL to facilitate background subtraction and data analysis |
|
EMBL |
Program suite for small-angle scattering data analysis from biological macromolecules - https://www.embl-hamburg.de/biosaxs/software.html |
|
|
BioXTAS |
Program for analysis of Small-Angle X-ray Scattering (SAXS) data - https://bioxtas-raw.readthedocs.io/en/latest/api.html |
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Schrödinger |
Molecular visualization system - https://pymol.org/2/ |
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UCSF |
Interactive visualization and analysis of molecular structures - https://www.cgl.ucsf.edu/chimera/ |
Software required for Session 2
|
Software |
Source |
Application |
|
Irena |
Igor Pro* |
Irena package for analysis of small-angle scattering data |
|
SASView 5+ |
SASView for small-angle scattering analysis - https://www.sasview.org |
A free demonstration version of Igor Pro is available at [https://www.wavemetrics.com/downloads/current/Igor%20Pro%209]]. This should be installed prior to installing the Irena package.
If you have any trouble to install the SANS Super EASY please contact Alan Hicks (hicksac@ornl.gov) and Wellington Leite (leitewc@ornl.gov) :
Installing the SANS Super EASY GUI:
This code uses python, and it is recommended that you install a new virtual environment using your favorite python virtual environment handling software.
If you have:
Mamba/Conda Install:
1. mamba/conda create -n sasgui -c conda-forge python=3.12
2. mamba/conda activate sasgui
3. mamba/conda install numpy pandas scipy param holoviews panel param bokeh
From the same virtual environment, we need to use pip to install the sasview code (https://github.com/sasview). Alternatively, pip can be used to install all the modules from 3.
4. pip install sasview sasdata sasmodels
Get the code from the GitLab repository:
5. git clone https://code.ornl.gov/rys/sans-analysis.git
This will create a file sans-analysis in your local machine with a file, “canvas.py”
Run the command:
6. python3 sans-analysis/canvas.py
This will open a web-based GUI for running the analysis.
If you do not have git or do not know how to use git, we are going to use a jupyter notebook to launch the GUI.
7. In addition to the above module installs, we need to install jupyer and jupyter notebook.
8. mamba/conda/pip install jupyter notebook
Go to the following link to copy the code for the SANS Super EASY GUI:
https://colab.research.google.com/drive/1bo4wSZUkgWvhS5TWzql02aokXjfNnRGD?usp=sharing
Copy the code to a new notebook and then run all cells. Alternatively, you can copy the code to a new file, canvas.py and run like 6 above.
