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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 setupSetup datasets
For the reference structure, you will need to:
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All the dataset folders and your reference dataset should be in the one folder, where you will run CXASAP.
Setup 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:
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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.
It will also print out a description of each of the fields in the conf.yaml file which you need to fill out:
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Open the conf.yaml file and add the details for your datasets. The main fields you need to fill in are the experiment_location and the reference_path.
Most importantly, the experiment location is the path to the folder containing all your datasets, while the reference path is the path to the .ins or .res file for your reference.
Be aware that if/when you run the --configure command again for any pipeline, it will overwrite this file. So you might want to save a copy in your dataset folder if you think you will want to use it again, like if you are going to use a different reference file.
Run CXASAP!
Now you should be able to run pipeline-refinement easily
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You should see the output of shelxl running in powershell.
Wait patiently for it to finish.
Check the output
You can look at the error_output.txt or refinement_summary.txt files in the folder with all your datasets. This will tell you if there are structures that did not converge, or if other errors occurred.
If there are multiple structures that have not converged, try increasing the maximum cycles and the refinements in the conf.yaml file, and running pipeline-refinement again. You can also open the .res files for the structures that did not refine to convergence and see if they are looking sensible or have solved/refined to nonsense. If that is the case, you will need to refine them manually. But after you do this and have all your cifs ready, providing they stay in the same space group as the reference structure, you can move on to pipeline-cif