LCLS 2022 User Meeting workshop

Applications for small-molecule Serial Femtosecond Diffraction in Materials Science and Chemistry

This repository holds the software for the tutorials used during the LCLS 2022 user meeting workshop on the topic of Applications for small-molecule Serial Femtosecond Diffraction in Materials Science and Chemistry.

The full documentation for the workshop, including tutorials and links to the dataset is here.

Installation

There are installers for each platform. You can run the installer on linux and macOS by typing

chmod u+x cctbx.xfel-<version>-<platform>-<architecture>.sh
./cctbx.xfel-<version>-<platform>-<architecture>.sh -b -p <prefix>

Then add the bin directory to your path in bash with

export PATH=<prefix>/bin:${PATH}

or in csh with

setenv PATH <prefix>/bin:${PATH}

For Windows, run the executable and select a directory for installation. To add the commands to your %PATH% in the Command Prompt, type

set PATH=<installation path>\Library\bin;<installation path>\Scripts;<installation path>;%PATH%

By default, the <installation path> is C:\Users\<user name>\cctbx.xfel. The commands exist in 3 locations which is why 3 directories are added to the %PATH%.

Juptyer Notebook

Once the software is installed and your path updated, you can start Jupyter lab with

jupyter lab

Advanced Usage

The installed software is essentially a conda environment, so if you have conda installed, you can activate the environment with

conda activate <prefix>/

Then you can modify or add dependencies.