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pipeline-refinement This module will refine a series of structures to convergence based on a single reference file. Such a dataset might have come from a dynamic experiment, such as variable-temperature, variable-pressure, variable-position, etc | SHELXL | You require the below 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 | 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
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pipeline-cif This pipeline will merge a series of CIF files with instrument CIFs. All CIFs will then be combined and run through checkCIF. | platon | You require the below files: This series of folders should be in one parent folder
This parent folder can be located anywhere
Your instrument CIFs will either need the same name, or a common file ending that is not just .cif. For example, Rigaku instruments have .cif_od as their instrument CIF | Descriptions are listed below: chemical_formula: enter the chemical formula crystal_habit: enter the habit of your crystal crystal_colour: describe the colour of your crystal experiment_location: full path to the folder containing all folders with CIFs instrument_ending: if your instrument CIFs have different names but a common ending, list it here (ie .cif_od). If not, enter False instrument_file: if your instrument CIFs have identical names and endings, enter it here. If not, enter False max_crystal_dimension: largest dimension of your crystal middle_crystal_dimension: middle dimension of your crystal min_crystal_dimension: smallest dimension of your crystal structure_solution: list the structure solution software used
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pipeline-cif-combine This pipeline will combine a series of CIFs into one file. No edits will be made, but a checkCIF report will be given. | platon | You require the below files: | Descriptions are listed below: |
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pipeline-variable-analysis This pipeline will analyse .cif files for a dynamic experiment where one parameter in the cif files is changing. For example, this might be a change in temperature, pressure, etc. It will output graphs displaying changes in unit cell parameters and defined structural changes. | none | You require the below files: | Descriptions are listed below: 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 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
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pipeline-general This pipeline will refine a series of .hkl/.ins files based on a common reference and provide finalised .cif files, checkCIF reports and structural analysis. Use this only if your files are already in the correct directory structure (check by adding --files to command). Otherwise, consider 'pipeline-general-extra' | | You require the below files: Your .hkl/.ins files should be in separate folders located in a single parent folder
Your reference .cif file should be located anywhere outside of the individual .hkl/.ins folders
Your reference .cif file should contain all required crystal/instrument parameters | Descriptions are listed below: ADP_analysis: enter True for ADP analysis, otherwise enter False atoms_for_analysis: enter the atom labels for graphical structural analysis as a list (best suited to small numbers to avoid over cluttering graphs cif_parameters: enter the parameters to be extracted from your cifs - the default parameters are usually fine experiment_location: enter the full path to the folder containing your data sets maximum_cycles: enter the max number of cycles shelxl can run reference_cif_location: enter the full path to your reference .cif file refinements_to_check: enter the number of refinements you want to check for convergence structural_analysis_bonds: enter True for bond length analysis, otherwise enter False structural_analysis_angles: enter True for angle analysis, otherwise enter False structural_analysis_torsions: enter True for torsion analysis, otherwise enter False - note that this will have required the CONF command in your reference .ins/.res file tolerance: enter the desired mean shift for the number of refinements in refinements_to_check varying_cif_parameter: enter the parameter in your cif files that is varying in proper cif syntax (ie _diffrn_ambient_temperature) varying_parameter_values: enter the values of your varying parameter as a list with errors. Ie if you did a VT experiment at 100(2)K and 200(2)K, enter 100(2) and 200(2) in the provided list
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pipeline-general-extra This pipeline will refine a series of .hkl/.ins files based on a common reference and provide finalised .cif files, checkCIF reports and structural analysis. This version of the script will set up folders for you based on your configuration file. You will be prompted to place your structure files in the folders created by the code. This version of the script also runs off the assumption you do not have a completed reference cif with all instrument parameters. Instead, you will be able to enter them into the configuration file. | | You require the below files: Your .hkl/.ins files can be anywhere, but you will need to put them in the folders the code creates
Your reference .ins/.res file should be located anywhere outside of the individual .hkl/.ins folders | Descriptions are listed below: atoms_for_analysis: enter the atom labels for graphical structural analysis as a list (best suited to small numbers to avoid over cluttering graphs cif_parameters: enter the parameters to be extracted from your cifs - the default parameters are usually fine experiment_location: enter the full path to the folder containing your data sets maximum_cycles: enter the max number of cycles shelxl can run reference_location: enter the full path to your reference .ins/.res file refinements_to_check: enter the number of refinements you want to check for convergence structural_analysis_bonds: enter True for bond length analysis, otherwise enter False structural_analysis_angles: enter True for angle analysis, otherwise enter False structural_analysis_torsions: enter True for torsion analysis, otherwise enter False - note that this will have required the CONF command in your reference .ins/.res file tolerance: enter the desired mean shift for the number of refinements in refinements_to_check varying_cif_parameter: enter the parameter in your cif files that is varying in proper cif syntax (ie _diffrn_ambient_temperature) varying_parameter_values: enter the values of your varying parameter as a list with errors. Ie if you did a VT experiment at 100(2)K and 200(2)K, enter 100(2) and 200(2) in the provided list
IMPORTANT NOTE: there are also a series of cif parameters listed
To minimise checkCIF alerts, fill these in
You can remove or add cif parameters as long as correct CIF syntax is used! |
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module-cif-read This module will extract data from a series of CIF files and output them into a .csv file. Examples of parameters for output include (but are not limited to) unit cell parameters and quality statistics. | none | You require the below files: | Descriptions are listed below: ADP_analysis: enter 'true' if you want to extract ADP information, otherwise enter 'false' 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 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
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module-cif-merge This module will merge one instrument CIF with one structure cif. This is useful if it was not done automatically through your structure solution/refinement software. CheckCIF will also be run to quickly validate the output. | platon | You require the below files: instrument cif structure cif
These files can be located anywhere | Descriptions are listed below: |
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module-ADP analysis This module will analyse the ADPs that have been previously extracted from CIF files. It is recommended that you run this AFTER module-cif-read OR use a pipeline with this included | none | You require the below files: | Descriptions are listed below: cell_path: Enter the path to the .csv file containing extracted unit cell data (recommended you run module-cif-read first!) csv_path: Enter the path to the .csv file containing extracted ADP data (recommended you run module-cif-read first)
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module-cell-analysis This module will analyse changes in the unit cell from a .csv file. If you have already run the cif reading module, then the file should be in the correct format. | none | You require the below files: This file can be located anywhere | Descriptions are listed below: csv_location: full path to your .csv file reference_unit_cell: enter the neutral unit cell for datasets to be compared to x_axis_header: enter the column title for your independent variable (ie temperature or pressure)
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module-make-instrument-cif This module will create an instrument CIF from a fully completed structural CIF file. It might be useful. It might not be. The option is there for you to use. | none | You require the below files: This file can be located anywhere | Descriptions are listed below: |
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module-refinement This module will refine a single structure to convergence using a single reference file. | SHELXL | You require the below files: Your .hkl/.ins file should be in the same folder
Your reference .ins/.res file can be located anywhere | Descriptions are listed below: 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 structure_location: enter the full path to your new .ins file tolerance: enter the desired mean shift for the number of refinements in refinements_to_check
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module-rotation-planes For a single dataset refined with the MPLA command, the angle to a reference plane can be calculated. To automatically analyse a series of files, use the rotation pipeline. | none | You require the below files: This file can be located anywhere | Descriptions are listed below: lst_file_location: enter the full path to your lst file for analysis reference_plane: fill out the list with the three numbers that form your reference crystallographic plane. For example, to compare to the (100) plane, enter the three numbers '1', '0', and '0' in the three positions.
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module-structural-analysis This module will examine structural data in .csv files and separate/graph
the important parts of interest. For example, if you are investigating the spin-crossover properties of a metal complex, you might be most interested in the M-L bond lengths. By specifying the metal atom, you graphs will be provided and a separated spreadsheet of those bonds will be provided. This module currently requires the use of the 'cif_read' module prior. | none | You require the below files: a .csv file of your bond data a .csv file of your angle data a .csv file of your torsion data
Note that do you not need all of these files present
These files can be located anywhere | Descriptions are listed below: angle_data: enter the full path to your angle .csv file (or false if you do not have one) atoms_for_analysis: enter the label of the atoms you are most interested in bond_data: enter the full path to your bond .csv file (or false if you do not have one) torsion_data: enter the full path to your torsion .csv file (or false if you do not have one)
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