mmCIF dictionary

[multimeric]

When I run cif-validate (or indeed any other cif-tools binary) on AlphaFill files, I get a number of validation errors. I wonder if you're using a custom dictionary? If yes, can you provide it so that these tools work properly?

As an example:

$ curl -L https://alphafill.eu/v1/aff/P04406-F1 > P04406-F1.cif                                                                                              (base) 
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  354k  100  354k    0     0   151k      0  0:00:02  0:00:02 --:--:--  151k
$ cif-validate --verbose P04406-F1.cif                                                                                                                       (base) 
Error validating database_id: When validating _database_2.database_id: Value 'AF' is not in the list of allowed values
undefined Category ma_data
undefined Category ma_model_list
undefined Category ma_qa_metric
undefined Category ma_qa_metric_global
undefined Category ma_qa_metric_local
undefined Category ma_software_group
undefined Category ma_target_entity
undefined Category ma_target_entity_instance
undefined Category ma_target_ref_db_details
missing mandatory field dict_version for Category audit_conform
Error validating database_id: When validating _database_2.database_id: Value 'AF' is not in the list of allowed values
undefined Category ma_data
undefined Category ma_model_list
undefined Category ma_qa_metric
undefined Category ma_qa_metric_global
undefined Category ma_qa_metric_local
undefined Category ma_software_group
undefined Category ma_target_entity
undefined Category ma_target_entity_instance
undefined Category ma_target_ref_db_details
missing mandatory field dict_version for Category audit_conform
CPU usage: 0.8s user, 0.0s system, 0.0s wall

[mhekkel]

Thanks for that question! Never took the time to investigate this. Anyway, the dictionary can be found at:

https://github.com/ihmwg/ModelCIF

And when using this I see that the AlphaFold files are not valid at all. The key for ma_qa_metric_local is ordinal_id and this field contains the value 1 for all records. Obviously that's wrong. I guess I will have to report this as a bug at AlphaFold.

[multimeric]

Thanks! That's still helpful, I should be able to just adjust the alphafold CIFs to make them conform to your dictionary.

[multimeric]

Okay so actually the new alphafold structures don't have this issue. The v3 ones in AlphaFold DB have the correct ordinal_id:

$ curl 'https://alphafold.ebi.ac.uk/files/AF-P00519-F1-model_v3.cif' | grep -A 10 'ma_qa_metric_local'                                                      _ma_qa_metric_local.label_asym_id
_ma_qa_metric_local.label_comp_id
_ma_qa_metric_local.label_seq_id
_ma_qa_metric_local.metric_id
_ma_qa_metric_local.metric_value
_ma_qa_metric_local.model_id
_ma_qa_metric_local.ordinal_id
A MET 1    2 31.65 1 1    
A LEU 2    2 35.05 1 2    
A GLU 3    2 36.20 1 3    
A ILE 4    2 52.07 1 4    
A CYS 5    2 39.89 1 5    
A LEU 6    2 47.68 1 6    
A LYS 7    2 45.71 1 7    
A LEU 8    2 38.50 1 8    
A VAL 9    2 42.44 1 9    
A GLY 10   2 31.30 1 10   

So if you guys rerun the alphafill analysis at some point, this should be fixed.