Retrieving validation data for EMDB entry: EMD-71610
Client: <emdb.client.EMDB object at 0x1028414c0>
Traceback (most recent call last):
File "/xxx/lib/python3.12/site-packages/emdb/client.py", line 60, in get_validation
return EMDBValidation.from_api(emdb_id, data, self)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/xxx/lib/python3.12/site-packages/emdb/models/validation.py", line 360, in from_api
scores=EMDBValidationScores.from_api(data),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/xxx/lib/python3.12/site-packages/emdb/models/validation.py", line 190, in from_api
EMDBModelScore.from_atom_inclusion(all_atom_inclusion_by_level[model_index], all_residue_inclusion[model_index])
File "/xxx/lib/python3.12/site-packages/emdb/models/validation.py", line 142, in from_atom_inclusion
raise ValueError(f"Unexpected residue format: {r}")
ValueError: Unexpected residue format: H:-44 DG
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/xxx/lib/python3.12/site-packages/emdb/models/entry.py", line 153, in get_validation
return self._client.get_validation(self.id)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/xxx/lib/python3.12/site-packages/emdb/utils.py", line 19, in wrapper
result = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/xxx/lib/python3.12/site-packages/emdb/client.py", line 64, in get_validation
raise EMDBAPIError(f"Failed to retrieve validation for {emdb_id}: {str(e)}")
emdb.exceptions.EMDBAPIError: EMDB API Error: Failed to retrieve validation for EMD-71610: Unexpected residue format: H:-44 DG
Can't see what's wrong here - the associated atomic model (9pfq) has a deoxyguanosine -44 in chain H but I don't understand why that shouldn't be handled.
ATOM 28637 P P . DG G 6 8 ? 298.041 317.623 205.684 1.00 207.71 ? -44 DG H P 1
ATOM 28638 O OP1 . DG G 6 8 ? 299.157 318.591 205.767 1.00 207.71 ? -44 DG H OP1 1
ATOM 28639 O OP2 . DG G 6 8 ? 297.989 316.471 206.611 1.00 207.71 ? -44 DG H OP2 1
ATOM 28640 O "O5'" . DG G 6 8 ? 296.654 318.413 205.796 1.00 207.71 ? -44 DG H "O5'" 1
ATOM 28641 C "C5'" . DG G 6 8 ? 296.095 318.699 207.075 1.00 207.71 ? -44 DG H "C5'" 1
ATOM 28642 C "C4'" . DG G 6 8 ? 294.784 319.451 206.934 1.00 207.71 ? -44 DG H "C4'" 1
ATOM 28643 O "O4'" . DG G 6 8 ? 293.945 318.767 205.975 1.00 207.71 ? -44 DG H "O4'" 1
ATOM 28644 C "C3'" . DG G 6 8 ? 293.945 319.518 208.196 1.00 207.71 ? -44 DG H "C3'" 1
ATOM 28645 O "O3'" . DG G 6 8 ? 293.033 320.606 208.112 1.00 207.71 ? -44 DG H "O3'" 1
ATOM 28646 C "C2'" . DG G 6 8 ? 293.217 318.180 208.154 1.00 207.71 ? -44 DG H "C2'" 1
ATOM 28647 C "C1'" . DG G 6 8 ? 292.960 318.008 206.656 1.00 207.71 ? -44 DG H "C1'" 1
ATOM 28648 N N9 . DG G 6 8 ? 293.056 316.623 206.204 1.00 207.71 ? -44 DG H N9 1
ATOM 28649 C C8 . DG G 6 8 ? 294.199 315.940 205.863 1.00 207.71 ? -44 DG H C8 1
ATOM 28650 N N7 . DG G 6 8 ? 293.978 314.709 205.493 1.00 207.71 ? -44 DG H N7 1
ATOM 28651 C C5 . DG G 6 8 ? 292.601 314.566 205.594 1.00 207.71 ? -44 DG H C5 1
ATOM 28652 C C6 . DG G 6 8 ? 291.779 313.447 205.324 1.00 207.71 ? -44 DG H C6 1
ATOM 28653 O O6 . DG G 6 8 ? 292.118 312.323 204.929 1.00 207.71 ? -44 DG H O6 1
ATOM 28654 N N1 . DG G 6 8 ? 290.435 313.727 205.556 1.00 207.71 ? -44 DG H N1 1
ATOM 28655 C C2 . DG G 6 8 ? 289.948 314.935 205.995 1.00 207.71 ? -44 DG H C2 1
ATOM 28656 N N2 . DG G 6 8 ? 288.619 315.016 206.162 1.00 207.71 ? -44 DG H N2 1
ATOM 28657 N N3 . DG G 6 8 ? 290.706 315.992 206.252 1.00 207.71 ? -44 DG H N3 1
ATOM 28658 C C4 . DG G 6 8 ? 292.018 315.735 206.030 1.00 207.71 ? -44 DG H C4 1
ATOM 28643 P DG H -44 298.041 317.623 205.684 1.00207.71 P
ATOM 28644 OP1 DG H -44 299.157 318.591 205.767 1.00207.71 O
ATOM 28645 OP2 DG H -44 297.989 316.471 206.611 1.00207.71 O
ATOM 28646 O5' DG H -44 296.654 318.413 205.796 1.00207.71 O
ATOM 28647 C5' DG H -44 296.095 318.699 207.075 1.00207.71 C
ATOM 28648 C4' DG H -44 294.784 319.451 206.934 1.00207.71 C
ATOM 28649 O4' DG H -44 293.945 318.767 205.975 1.00207.71 O
ATOM 28650 C3' DG H -44 293.945 319.518 208.196 1.00207.71 C
ATOM 28651 O3' DG H -44 293.033 320.606 208.112 1.00207.71 O
ATOM 28652 C2' DG H -44 293.217 318.180 208.154 1.00207.71 C
ATOM 28653 C1' DG H -44 292.960 318.008 206.656 1.00207.71 C
ATOM 28654 N9 DG H -44 293.056 316.623 206.204 1.00207.71 N
ATOM 28655 C8 DG H -44 294.199 315.940 205.863 1.00207.71 C
ATOM 28656 N7 DG H -44 293.978 314.709 205.493 1.00207.71 N
ATOM 28657 C5 DG H -44 292.601 314.566 205.594 1.00207.71 C
ATOM 28658 C6 DG H -44 291.779 313.447 205.324 1.00207.71 C
ATOM 28659 O6 DG H -44 292.118 312.323 204.929 1.00207.71 O
ATOM 28660 N1 DG H -44 290.435 313.727 205.556 1.00207.71 N
ATOM 28661 C2 DG H -44 289.948 314.935 205.995 1.00207.71 C
ATOM 28662 N2 DG H -44 288.619 315.016 206.162 1.00207.71 N
ATOM 28663 N3 DG H -44 290.706 315.992 206.252 1.00207.71 N
ATOM 28664 C4 DG H -44 292.018 315.735 206.030 1.00207.71 C
Getting validation information for EMD-71610 fails with the following traceback:
Can't see what's wrong here - the associated atomic model (9pfq) has a deoxyguanosine -44 in chain H but I don't understand why that shouldn't be handled.
mmCIF:
PDB: