CXASAP - pipelines and modules summary

SHELXL

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

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

platon

You require the below files:

• a series of folders, each containing a new CIF and an instrument CIF

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

platon

You require the below files:

• a series of CIF files in a single folder

Descriptions are listed below:

• location_of_cifs: the full path to the folder containing all CIF files

none

You require the below files:

• a series of .cif files located in a single folder

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

• SHELXL

• platon

• shredCIF

You require the below files:

• a reference .cif 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 .cif file should be located anywhere outside of the individual .hkl/.ins folders
Your reference .cif file should contain all required crystal/instrument parameters

You will need to fill out the 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

• SHELXL

• platon

• shredCIF

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 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

You will need to fill out the parameters.
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!