Diffraction Simulator

Standalone viewer associated with Methods in Enzymology Volume 687

Supported platforms. Optimal performance requires Linux_x86_64, accelerated with an Nvidia GPU, either Volta or Ampere architecture.

Installation. Please navigate on this page to the "+1 release" URL. There follow the instructions for download and install. Find the binary bundle listed under "Assets" and click the link for the cctbx.xfel-2023.5.26-Linux-x86_64.sh.

Running the program. Start from the command line with:

simtbx.sim_view

Documentation. Read the docs on Github at the sim_erice page including explanations of the controls and the tunable parameters. You can also launch the viewer with -h or --help to see the help message. More details on which parameters are tunable is visible by typing:

simtbx.sim_view -c -e5 -a2

Community input. The source code repository makes provision for users to report bugs, request features, and contribute code.

Developer build. Find the source bundle listed under "Assets" and click the link for Source code

Google Colab notebook

Due to mismatched CUDA driver versions between Google Colab and conda, the notebook is not currently functional. Please check back.

Jupyter notebook

Future implementation as a Jupyter notebook is contemplated.

Erice 2022 International School of Crystallography, 57th Course

Diffuse Scattering: The Crystallography of Dynamics, Defects, and Disorder

This repository holds the software for the tutorials used during the 2022 International School of Crystallography held in Erice, Italy on the topic of Diffuse Scattering: The Crystallography of Dynamics, Defects, and Disorder.

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%.

Installer Notes

The installers for Apple Silcon (MacOSX-arm64) and Windows do not have dependencies for molecular dynamics.

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.