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Background

CXASAP is a software project designed to reduce the time required for analysis of serial crystallography experiments. Using a reference structure, it can refine, finalise and compare datasets with a range of temperatures and pressures.

Before you start

You will need CXASAP, and some other accompanying software, installed on your computer.

See CXASAP Windows Installation Instructions for instructions for installing on Windows.

See https://cx-asap.github.io/USER.html#installation for instructions for installing on Linux.

Running CXASAP

CXASAP runs via a terminal, where you will input instructions about the module or pipeline you want to run.

After it is installed, if you open a terminal and activate the virtual environement and run this command: 

cxasap

Read the output in the terminal and it will guide you how to run the code.

Step 1. Pipeline-refinement

This pipeline will refine a series of datasets based on a single reference structure, which would likely be your ambient structure or the lowest pressure structure. Although if there is a phase change or significant changes in this structure, you may want to use a reference in the middle of the pressure series. If you don;t think refining your datasets based on a single reference structure will be helpful, you can skip to Step 2: pipeline-cif

Dataset setup

For the reference structure, you will need to:

  • Refine it to convergence

  • Label the atoms, especially those you are interested in throughout the series

  • DO NOT use the solvent mask or SQUEEZE. This will confuse CXASAP because it will look for a fab file. If your structure is porous, just refine it as best you can without SQUEEZE or a solvent mask. If you need to refine it with a solvent mask for publication, you will need to do it manually after you do the parallel refinement. 

  • Place the ins, res, hkl and cif files in a folder together. 

For the datasets, you will need a folder for each, which includes its hkl and ins files.

All the dataset folders and your reference dataset should be in the one folder, where you will run CXASAP.

CXASAP setup

If you are running pipeline-refinement the first thing you want to do is run the help command in CXASAP, which should look like this:

You can check the files required, by running this command:

cxasap pipeline-refinement --files

Then you want to configure CXASAP for this pipeline, by running this command:

cxasap pipeline-refinement --configure

This will make a new file called conf.yaml in the cx_asap folder, which is in your CX-ASAP-main folder where you installed the software.

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