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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 finish off the refinement 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-variable-analysis. At this step, don’t add any information under _refine_special_details as this will upset the next step.
Step 2. Pipeline-variable-analysis
To extract all the structural information your heart may desire from the cifs you have just made, you want to run pipeline-variable-analysis through cxasap
Collect cifs into a single folder
In order to run the pipeline that will compare the structures based on their cifs, you need to copy all the cifs into the same folder, and give them unique names, probably naming them by their pressure would be the best bet.
Add pressure values to cif
You will need to add a field to each of your cifs with the pressure of the experiment. Keep the units consistent (either GPA or Pa) and only add a number, not the units.
It should look like this:
_diffrn_ambient_pressure 150000
You can add it anywhere in your cif, but best practice would be to add it after _diffrn_ambient_temperature
Configure pipeline-variable-analysis
Go back to your powershell in the CX-ASAP-main folder, where you have the virtual environment activated.
Configure pipeline-variable-analysis
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Open the new conf.yaml file in the cx_asap folder, and edit it with your experiment details.
The parameters you need to fill out are these:
ADP_analysis: enter 'true' if you want to extract ADP information, otherwise enter 'false'
atoms_for_analysis: enter the label of the atoms you are most interested in
cif_parameters: these are the parameters that will be extracted from the cif - default ones are usually enough - note that any additional ones must be written in exact cif format
experiment_location: enter the full path to the folder which contains your .cif files
reference_unit_cell: enter the path to a reference .ins file. This could be your ambient dataset, or first pressure point.
structural_analysis_bonds: enter 'true' if you want to extract bond information, otherwise enter 'false'
structural_analysis_angles: enter 'true' if you want to extract angle information, otherwise enter 'false'
structural_analysis_torsions: enter 'true' if you want to extract torsion information, otherwise enter 'false' - note that cif files will only contain this information if you refined your structures with the 'CONF' command
varying_cif_parameter: enter the parameter in your .cif files that is changing. Make sure you use proper .cif syntax (for high pressure, it will be
_diffrn_ambient_pressure)
You can change the ADP_analysis, structural_analysis_angles, structural_analysis_bonds and structural_analysis_torsions from false to true if you want to extract the information on these parameters. Generally you may as well make them all true. Unless you have isotropic atoms in your reference structure, in which case leave ADP_analysis as false.
For example the conf.yaml will look something like this:
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Now you can run the analysis!
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After it has run you should have png files of graphs of bond lengths and angles etc. And the raw data that has been extracted will be in .csv files. These can be opened in excel if you want to select specific data to make graphs.
The bond lengths, angles and torsions from the atoms which you listed under “atoms_for_analysis” in the conf.yaml will be in the _Important_Bond_Angles, _Important_Bond_Lengths and _Important_Bond_Torsions files in the folder with your cifs. All others will be in subfolders called _Individual_Angle_Data, _Individual_Bond_Length_Data and _Individual_Torsion_Data.
Step 3. Enjoy your data analysis and write lots of papers!
And don't forget to reference CXASAP https://doi.org/10.1107/S1600576723000298