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Basics

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, activate the virtual environment and run this command:

cxasap

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:

cxasap pipeline-or-module --argument

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)

Example

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

First, I check the dependencies:

cxasap pipeline-refinement --dependencies

This will give the following text in the terminal:

You require the below software in your path:
- SHELXL

Then I will check the files required:

cxasap pipeline-refinement --files

Which will give me this:

You require the below files:
 - a reference .ins or .res file
 - a series of .hkl files
 - a series .ins files corresponding to the .hkl files

Your .hkl/.ins files should be in separate folders located in a single parent folder
Your reference .ins/.res file should be located outside of the individual .hkl/.ins folders

Then I want o configure cxasap for this pipeline

cxasap pipeline-refinement --configure

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.

Writing a file called conf.yaml in the cx_asap folder...

You will need to fill out the parameters.
Descriptions are listed below:
 - experiment_location: enter the full path to the folder containing all dataset folders
 - maximum_cycles: enter the max number of cycles shelxl can run
 - reference_path: enter the full path to your reference .ins or .res file
 - refinements_to_check: enter the number of refinements you want to check for convergence
 - tolerance: enter the desired mean shift for the number of refinements in refinements_to_check