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flr2mmcif

The python script converts the information in the filled spreadsheet template to a mmcif file for PDB-Dev. This includes the part for the fluorescence (flrCIF) dictionary.

Requirements

The script requires Python3 with ihm, and pandas installed.

Usage

1. Fill the spreadsheet (xls_template.xlsx).

  • Please fill all tabs as complete as possible. Omitting important parts of the spreadsheet will result in failure of the script.
  • Each row has a unique ID in the first column. This has to be filled.
  • Please do not change the headers of the columns (in particular row 4). Thus, only rows from number 5 on should be modified and filled.
  • Please do not modify the names of the tabs in the spreadsheet, as the python script relies on the names.
  • Ideally fill the tabs from the first to the last, since some of the tabs provide selections based on the other tabs.

2. Prepare an mmcif file for the atomic coordinates for the structural models.

  • Please make sure that the atomic coordinates are provided in the order of the models in the Models tab in the spreadsheet. This will not be checked by the conversion script.
  • The mmcif file must at least contain _atom_site entries. Additionally, _ihm_model_list, _ihm_model_group and _ihm_model_group_link entries can be provided and will then be used.

3. Run the python script, e.g.

python3 flr2mmcif.py --xls xls_example.xlsx --atoms atom_site_input_example.cif --cif output_filename.cif

Arguments for the script:

  • --xls or -x: The spreadsheet file based on the xls_template.xlsx
  • --atoms or -a: The cif file containing the _atom_site entries for the structural models.
  • --cif or -c: The name of the output file to be generated by the script.

4. After generation, it is recommended to check the resulting mmcif file whether the output is what was expected.

Documentation

An overview of the content in the spreadsheet can be found in Documentation

References

The python-ihm package and the IHMCIF and flrCIF dictionaries can be found on https://github.com/ihmwg

PDB-Dev: https://pdb-dev.wwpdb.org/