Data Reduction Workshop for the 2022 Erice International School of Crystallography

These materials were developed for the 2022 Erice School on Diffuse Scattering: https://crystalerice.org/2022/programme_ds.php

Overview

The workshop is 1.5 hours and is divided into 6 self-guided tutorials.

We will introduce modern diffuse scattering data reduction techniques using three open-source python packages:

• dials for Bragg peak indexing and geometry refinement
• mdx2 for image processing and reciprocal space reconstruction
• nexpy for visualization

The tutorials are:

1. Indexing Bragg diffraction data with DIALS
2. Exploring diffraction geometry using mdx2 and nexpy
3. Processing diffraction images with mdx2
4. Diffuse scattering integration with mdx2
5. Merging diffuse scattering with mdx2
6. Using mdx2 in python (advanced)

Requirements

The exercises are designed to run on a laptop computer with OSX, Linux, or Windows. You will need at least 10 Gb of free disk space for the python environment, tutorial data, and intermediate files.

If you are bringing your own laptop to Erice, please do the following before you travel:

1. Download insulin_2_1.tar from Zenodo

2. Install the Erice-2022 python environment for macromolecular crystallography (Link: https://github.com/cctbx-xfel/erice_2022)

3. Download the tutorials (Link: https://github.com/ando-lab/erice-2022-data-reduction/archive/refs/tags/v1.0.zip)

4. Download some pre-processed results (Link: https://github.com/ando-lab/erice-2022-data-reduction/releases/download/v1.0-alpha/corrected.nxs)

5. Follow the Installation instructions for mdx2, below.

Installation instructions for mdx2

1. Download mdx2 here: https://github.com/ando-lab/mdx2/archive/refs/tags/v0.3.0.zip

2. Unzip and move the folder mdx2-0.3.0 somewhere easy to find (such as ~/Documents/Erice).

3. Open a terminal window and add the Erice python environment to the path (Instructions here: https://github.com/cctbx-xfel/erice_2022). Change to the mdx2-0.3.0 directory, and run:

pip install -e .

This should work without errors (get in touch if you have issues).

4. Verify that mdx2 is installed by running:

mdx2.version

The current version number should be printed.

Quick start

1. Double-click insulin_2_1.tar. This will produce a folder called images with three subdirectories. Move the images folder to the tutorial directory (erice-2022-data-reduction-1.0).

2. Open a terminal window and make sure Erice python environment is on path (see above). Change to the tutorial directory (erice-2022-data-reduction-1.0) and type:

jupyter lab

Jupyter lab should open in your internet browser.

3. In the File Browser (left panel), double-click 1_dials_indexing.ipynb.