Comments (4)
The mediator.cif cr_mid_fullmed10.pdb has chains D,G,I,J,U,Z and is referenced as dataset_list_id=2 by five starting models which have asym_id H,I,J,K,L.
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Is it assumed that the sequence numbers for dataset_list models referred to in the starting_model_details table exactly match the sequence numbers used by the sphere models (given by seq_id_begin and seq_id_end in the starting_model_details table?
If the sequence numbers are not required to match, then a correspondence between experimental/comparative input models and the sphere model sequence numbers will be needed.
from ihmcif.
In the updated dictionary, _ihm_starting_model_details.starting_model_auth_asym_id
and _ihm_starting_model_details.starting_model_sequence_offset
address this issue.
from ihmcif.
I think we need the starting_model_db_auth_asym_id field in addition to the new starting_model_auth_asym_id field in _ihm_starting_model_details. The db_auth_asym_id tells which change of a database entry was used in a comparative alignment. The auth_asym_id tells which chain in the resulting comparative model file corresponds to the asym_id in the sphere model. In the case of nup84 the comparative model asym_ids match the sphere model asym_ids, but in the case of mediator.cif comparative model (cr_mid_fullmed10.pdb the asym_ids don't match the sphere model asym_ids. We were able to repurpose db_auth_asym_id to match these only because that comparative model did not list database templates, so the db_auth_asym_id was not being used.
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Related Issues (20)
- Add "starting model" to the enumeration list for `_ihm_dataset_group.application`
- Address redundant parent-child relationships in atom_site category
- Update CX-MS to Crosslinking-MS in the dictionary
- Expand ihm_cross_link_list table
- Rename `ihm_ensemble_info` category HOT 3
- Use cases of `multi-residue` `_ihm_model_representation_details.model_granularity`
- missing link between `_ihm_sphere_obj_site` and `_ihm_model_representation_details` HOT 3
- Remediation of jPOST IDs with ProteomeExchange
- Consider making _ihm_ensemble_info.model_group_id mandatory
- Add AlphaFoldDB to the list of databases HOT 3
- the data category 'ihm_ordered_ensemble' is misleading
- Add generic restraints
- Depositor-reported cross-linking satisfaction rates
- Dictionary update for Input dataset groups - Add modeling option for application
- Item type for `_ihm_dataset_related_db_reference.accession_code`
- Extend IHMCIF to add model_id to existing PDBx/mmCIF tables
- Updated descriptions of model related categories
- Allow for optional asym_id in tables where information can be the same across different instances of the same entity
- Allow for segments of branched entities to be defined and used in related categories
- Review parent-child relationships in ihm_starting_model_coord
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