CXASAP - serial data analysis

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 from variable temperature, photocrystallography, or high-pressure experiments.

Basics

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

After it is installed (Instructions here), if you open a terminal, activate the virtual environment and run this command:

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

The general command line for running CXASAP looks like this:

The arguments you can run for each module or pipeline are:

--dependencies (this will tell you the required software for this code to run)

--files (will tell you the required file structure/input files)

--configure (will write the yaml file for this pipeline/module in the cx_asap folder where you installed CXASAP. You will then need to open it and fill out the relevant information for your experiment)

--run (will execute the code)

Instruction pages:

CXASAP on MX

CXASAP Windows Installation Instructions

CXASAP Summary of pipelines and modules

Example

I want to run pipeline-refinement on a series of datasets.

First, I check the dependencies:

This will give the following text in the terminal:

Then I will check the files required:

Which will give me this:

Then I want o configure cxasap for this pipeline

Which will give me this in the terminal. This is a description of the fields that need to be filled out in the conf.yaml file.