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First draft of instructions for sim_view in Colab
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irisdyoung committed Feb 10, 2023
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# Diffraction Simulator
## Google Colab notebook associated with Methods in Enzymology Volume 687
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The quickest way to get started is to run the [Google Colab notebook](https://colab.research.google.com/drive/1dXWW7ptKDxWVmfMGFKeXq9cagALLH5i4?usp=sharing) directly from your browser. The compute nodes are hosted and allocated by Google, so you can simply connect with the default settings and begin executing cells. The first cells set up the environment (the notebook, a conda environment, and the cctbx.xfel installation) and the rest set up the simulation viewer. After running all the cells in order, you should see a set of widgets controlling the parameters of the diffraction experiment and an image of the simulation that updates in lockstep with these parameters. More detailed instructions can be found in the notebook itself.

## Jupyter notebook
As an alternative to the above, you can run a derivative of the Colab notebook using Jupyter. Download the Colab notebook -- this should already be an .ipynb file. Remove the cells at the very beginning that give instructions to Colab, and run the installation of cctbx.xfel in a conda environment locally instead, as follows: You will first need to install [conda](https://conda.io/projects/conda/en/stable/user-guide/install/download.html) and then run `conda install mamba`. Then you can run `mamba install -q -c xfel cctbx.xfel`. Activate the new conda environment and run Jupyter with the cctbx-xfel build of python. In the simplest case, this means running `jupyter-notebook simtbx.sim_view.ipynb`. The steps from "Load modules" onward should work identically to how they work in the Colab notebook.

## Standalone viewer
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The third option for running the simulation viewer is to do a standard installation of cctbx.xfel for Erice and run the viewer from the command line with `simtbx.sim_view`. See below for installation instructions. If you want a developer build and access to all the code, there are instructions to build from source in the Readme for the [cctbx project](https://github.com/cctbx/cctbx_project). Be sure to select the `xfel` builder if you follow those instructions.

# Erice 2022 International School of Crystallography, 57th Course
## Diffuse Scattering: The Crystallography of Dynamics, Defects, and Disorder
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