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After it is installed, if you open a terminal and , activate the virtual environement environment and run this command:
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cxasap |
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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
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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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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.
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Now you should be able to run pipeline-refinement easily
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