Comments (4)
Currently, all input data is listed in IHM_DATASET_LIST
. Data present in other databases are described in IHM_DATASET_RELATED_DB_REFERENCE
and those present in other resources are referenced via DOI in IHM_EXTERNAL_REFERENCE_INFO
and IHM_DATASET_EXTERNAL_REFERENCE_DETAILS
categories.
Localization density is an output from the I/H modeling and relates to the molecular system and the ensemble of good scoring models obtained from the modeling. Localization densities can be included as Gaussian mixture models in IHM_GAUSSIAN_OBJ_ENSEMBLE
or can be linked out via IHM_EXTERNAL_REFERENCE_INFO
and IHM_LOCALIZATION_DENSITY_FILES
categories.
Sequence alignments corresponding to the starting structural models can be included via IHM_EXTERNAL_REFERENCE_INFO
and IHM_STARTING_MODEL_ALIGNMENT_FILES
categories. We will also define categories to capture the alignments internally. This requires coordination with the PMP/Model Archive developers so that we are consistent with their definitions as well.
Modeling scripts, associated documentation and other workflow-related files can be referred to via IHM_EXTERNAL_REFERENCE_INFO
and IHM_MODELING_WORKFLOW_FILES
categories.
Wherever possible, we provide ways to incorporate data directly into the I/H model file and also provide the option to link out to external files in standard formats (eg: starting model coordinates, localization densities, alignments). The details of the linked out files are split into the different categories mentioned above because of the differences in the nature of the data that is stored in them. If these files and the data stored within are to be useful, they are best described in separate tables. The IHM_EXTERNAL_REFERENCE_INFO
table provides a way to collect the non-database external references is one place.
from ihmcif.
from ihmcif.
Reference to local file has been added.
from ihmcif.
A new category (IHM_EXTERNAL_FILES
) has been added to reference all external files.
from ihmcif.
Related Issues (20)
- 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
- 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
- Update all PDB-Dev references to PDB-IHM
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