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mmcif_ihm_ext.dic
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data_mmcif_ihm_ext.dic
_datablock.id mmcif_ihm_ext.dic
_datablock.description
;
This data block holds the extension dictionary for Integrative/Hybrid (I/H) methods.
This extension is based on the PDBx/mmCIF dictionary.
This resource is actively developed and maintained in a github repository available at
https://github.com/ihmwg/IHMCIF.
I/H structural models that are compliant to this extension dictionary can be deposited
to PDB-IHM (https://pdb-ihm.org).
;
#
_dictionary.title mmcif_ihm_ext.dic
_dictionary.datablock_id mmcif_ihm_ext.dic
_dictionary.version 1.27
#
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
0.000 2017-03-20
;
Changes (jdw/bv)
+ Release as initial version 0.000
+ Changed _imp to _ihm
+ Changed _imp_template_details to _ihm_starting_model_details
+ Changed _imp_tempate_model_coord to _ihm_starting_model_coord
+ Changed _imp_pseudo_atom_site to _ihm_sphere_object_site
+ Added enumeration 'integrative' to _ihm_starting_model_details.starting_model_source
+ Separated ihm_cross_link_restraint and ihm_cross_link_list categories
+ Updated ambiguous crosslinks in ihm_cross_link_restraint and ihm_cross_link_list categories
+ Added ihm_dataset_list, ihm_related_database_reference and ihm_dataset_other categories
+ Added ihm_cross_link_result (yet to be completed) and ihm_entity_assembly categories
+ Updated ihm_2dem_class_average_restraint category
+ Removed ihm_cross_link_db_reference, ihm_cross_link_reference_auxiliary, ihm_2dem_class_average categories
+ Revised several data items to be non-mandatory
+ Changed category key item in ihm_model_details category to account for multiple coarse-grained representations
of the same model segment (introduced _ihm_model_details.ordinal_id)
+ Updated _ihm_sphere_obj_site.entity_instance_id, ihm_cross_link_restraint (psi and sigma parameters)
+ Added ihm_modeling_protocol, ihm_cluster_info, ihm_struct_assembly (previously ihm_entity_assembly)
+ Added _ihm_3dem_restraint category; minor changes to other categories
+ Changed ihm_model_details category name to ihm_model_representation (handles multi-scale representation)
+ Changed several data items in the ihm_modeling_protocol category
+ Added ihm_modeling_post_process, ihm_model_list, ihm_multi_state_modeling,
ihm_time_ordered_ensemble, ihm_gaussian_object_site categories
+ Linked ihm_model_list to ihm_sphere_obj_site through model_id
+ Linked ihm_starting_model_details to ihm_dataset_list through dataset_list_id
+ Added new data item _ihm_model_representation.representation_id and more changes to ihm_modeling_protocol
and ihm_gaussian_obj_site categories.
+ Added ihm_gaussian_obj_ensemble category to represent ensembles as gaussian objects - to be different from
+ ihm_gaussian_object_site category that is used in model representation and hence by visualization software.
+ Changed ihm_cluster_info category name to ihm_ensemble_info and changed relevant data item names accordingly.
+ Changed ihm_related_database_reference category name to ihm_dataset_related_db_reference to be consistent
with other similar categories
+ Minor changes in other categories: ihm_model_list, ihm_dataset_list, ihm_modeling_protocol, ihm_ensemble_info,
ihm_multi_state_modeling, ihm_time_ordered_ensemble, ihm_2dem_class_average_restraint (data items are now
similar to 2D class average images in EMPIAR), ihm_model_represenation.
+ Updated parent-child relationships across several categories (ihm_modeling_protocol, ihm_ensemble_info
ihm_model_list, ihm_multi_state_modeling, ihm_time_ordered_ensemble, ihm_2dem_class_average_fitting,
ihm_cross_link_result)
+ Updated examples in ihm_dataset_list, ihm_dataset_other and ihm_dataset_related_db_reference
+ Changed ihm_modeling_experiment to ihm_modeling_protocol to be consistent with the model archive naming convention
+ Added ihm_sas_restraint category; added _ihm_3dem_restraint.map_segment_flag
+ Modified the following categories: ihm_model_list, ihm_modeling_protocol, ihm_multi_state_modeling,
ihm_time_ordered_ensemble
+ Minor updates to ihm_cross_link_list, ihm_cross_link_restraint and ihm_model_representation categories.
+ Added _ihm_sphere_obj_site.rmsf and _ihm_starting_model_details.asym_id
+ Added ihm_related_datasets and ihm_cross_link_result_parameters
+ Added _ihm_3dem_restraint.struct_assembly_id, _ihm_sas_restraint.struct_assembly_id,
_ihm_starting_model_details.notes and _ihm_starting_model_coord.group_PDB
+ Changed _ihm_3dem_restraint.id to _ihm_3dem_restraint.ordinal_id and _ihm_sas_restraint.id to
_ihm_sas_restraint.ordinal_id
+ Changed _ihm_dataset_related_db_reference.access_code to _ihm_dataset_related_db_reference.accession_code
+ Added new categories to reference externally hosted files: IHM_LOCALIZATION_DENSITY_FILES,
+ IHM_STARTING_MODEL_ALIGNMENT_FILES, IHM_MODELING_WORKFLOW_FILES
+ Added IHM_DATA_DOI_URL_INFO category to include a URL corresponding to a DOI. This enables automated
download of files.
+ Removed redundant DOI references from several categories
+ Added _ihm_starting_model_details.starting_model_sequence_offset
+ Changed _ihm_starting_model_details.starting_model_db_pdb_auth_asym_id to
_ihm_starting_model_details.starting_model_auth_asym_id
+ Changed IHM_DOI_URL_INFO to IHM_EXTERNAL_REFERENCE_INFO; modified all downstream dependencies
+ Changed IHM_DATASET_OTHER to IHM_DATASET_EXTERNAL_REFERENCE_DETAILS; modified all downstream dependencies
+ Modified definitions within IHM_EXTERNAL_REFERENCE_INFO
+ Added IHM_EXTERNAL_FILES category; Removed IHM_STARTING_MODEL_ALIGNMENT_FILES category
+ Changed IHM_MODELING_WORKFLOW_FILES, IHM_LOCALIZATION_DENSITY_FILES
+ Changed IHM_DATASET_EXTERNAL_REFERENCE_DETAILS to IHM_DATASET_EXTERNAL_REFERENCE
+ Modified IHM_STARTING_MODEL_DETAILS category
+ Added IHM_STARTING_COMPARATIVE_MODELS category
+ Added IHM_STARTING_MODEL_SEQ_DIF category; removed _ihm_starting_model_details.notes
+ Updated IHM_ENSEMBLE_INFO, IHM_EXTERNAL_FILES and IHM_EXTERNAL_REFERENCE_INFO
+ Added _ihm_multi_state_modeling.experiment_type; updated IHM_ENSEMBLE_INFO
;
0.100 2017-03-23
;
Changes (bv):
+ Release as provisional version 0.100
+ Added _ihm_external_files.content_type
+ Added _ihm_external_files.details
+ Removed IHM_MODELING_WORKFLOW_FILES
;
0.101 2017-03-29
;
Changes (bv):
+ Updated _ihm_starting_model_seq_dif.db_entity_id as non-mandatory
;
0.102 2017-03-29
;
Changes (bv):
+ Updated examples in IHM_STARTING_COMPARATIVE_MODELS
;
0.103 2017-03-30
;
Changes (bv):
+ Updated IHM_STARTING_MODEL_DETAILS
+ Updated IHM_STARTING_COMPARATIVE_MODELS
+ Updated IHM_DATASET_LIST, IHM_RELATED_DATASETS
+ Updated IHM_DATASET_RELATED_DB_REFERENCE
+ Updated IHM_DATASET_EXTERNAL_REFERENCE
+ Added examples to IHM_EXTERNAL_REFERENCE_INFO and IHM_EXTERNAL_FILES
;
0.104 2017-04-19
;
Changes (bv):
+ Updated IHM_STARTING_MODEL_DETAILS
+ Updated IHM_STARTING_COMPARATIVE_MODELS
+ Updated IHM_STARTING_MODEL_SEQ_DIF
+ Updated IHM_MODEL_REPRESENTATION
+ Updated IHM_DATASET_LIST
+ Added IHM_DATASET_GROUP
+ Updated IHM_MODELING_PROTOCOL
;
0.105 2017-05-25
;
Changes (bv):
+ Added item description to _ihm_ensemble_info.ensemble_file_id
+ Added item description to _ihm_2dem_class_average_restraint.pixel_size_width
+ Added item description to _ihm_2dem_class_average_restraint.pixel_size_height
+ Added category description to ihm_2dem_class_average_fitting
+ Added enumeration 'DCD' to _ihm_external_files.file_format
+ Changed _ihm_external_files.file_size_kb to _ihm_external_files.file_size_bytes
;
0.106 2017-07-13
;
Changes (bv):
+ Updated dictionary description and version history
;
0.107 2017-07-17
;
Changes (ep/bv):
+ Added category_group_list, item_type_list and item_units_list categories
;
0.108 2017-09-12
;
Changes (bv):
+ Added IHM_STRUCT_ASSEMBLY_CLASS, IHM_STRUCT_ASSEMBLY_CLASS_LIST
+ Added _ihm_struct_assembly.parent_assembly_id
;
0.109 2017-09-28
;
Changes (bv):
+ Added _ihm_model_list.representation_id
+ Added _atom_site.ihm_model_id
;
0.110 2017-10-03
;
Changes (bv):
+ Added _ihm_cross_link_restraint.atom_id_1, _ihm_cross_link_restraint.atom_id_2
+ Added _ihm_cross_link_restraint.restraint_type
+ Changed _ihm_cross_link_restraint.type to _ihm_cross_link_restraint.linker_type
+ Changed _ihm_cross_link_list.type to _ihm_cross_link_list.linker_type
+ Added enumerations to _ihm_cross_link_restraint.linker_type and _ihm_cross_link_list.linker_type
+ Added enumeration to and changed _item.mandatory_code of _ihm_cross_link_restraint.model_granularity
+ Added ihm_predicted_contact_restraint category
+ Added enumeration to _ihm_dataset_list.data_type
;
0.111 2017-10-04
;
Changes (bv):
+ Removed _ihm_cross_link_restraint.linker_type
+ Updated enumerations to _ihm_cross_link_restraint.restraint_type
;
0.112 2017-10-04
;
Changes (bv):
+ Added _ihm_dataset_list.details
+ Added enumeration to _ihm_dataset_list.data_type
;
0.113 2017-10-06
;
Changes (bv):
+ Added IHM_MODEL_REPRESENTATIVE
+ Added enumeration to _ihm_cross_link_list.linker_type
+ Updated item description for _ihm_predicted_contact_restraint.probability
;
0.114 2017-10-09
;
Changes (bv):
+ Fixed typos and syntax
;
0.115 2017-10-12
;
Changes (bv):
+ Added _ihm_modeling_post_process.feature_name
+ Fixed enumeration for _ihm_cross_link_list.linker_type
;
0.116 2017-10-16
;
Changes (bv):
+ Updated _item_description.description for _ihm_model_list.model_group_id
+ Updated enumerations for _ihm_dataset_list.data_type
+ Updated parent-child relationships within _ihm_model_list.model_id
;
0.117 2017-11-09
;
Changes (bv):
+ Updated description for _ihm_starting_model_details.starting_model_sequence_offset
;
0.118 2017-12-06
;
Changes (bv):
+ Changed ihm_time_ordered_ensemble to ihm_ordered_ensemble with appropriate revisions to the category
+ Changed _ihm_modeling_protocol.time_ordered_flag to _ihm_modeling_protocol.ordered_flag
+ Changed mandatory code for _ihm_model_list.representation_id
+ Added an example to ihm_model_list category
;
0.119 2017-12-07
;
Changes (bv):
+ Changed ihm_ordered_ensemble.ordered_process_id to ihm_ordered_ensemble.process_id
+ Changed ihm_ordered_ensemble.ordered_process_description to ihm_ordered_ensemble.process_description.
+ Changed parent-child relationships for _ihm_predicted_contact_restraint.atom_id_1,
_ihm_predicted_contact_restraint.atom_id_2, _ihm_cross_link_restraint.atom_id_1,
_ihm_cross_link_restraint.atom_id_2, _ihm_starting_model_coord.atom_id
;
0.120 2018-01-10
;
Changes (bv):
+ Added ihm_feature_selection_atom, ihm_feature_selection_residue, ihm_derived_distance_restraint
+ Fixed typos in the parent name of _ihm_predicted_contact_restraint.atom_id_1 and
_ihm_predicted_contact_restraint.atom_id_2
+ Fixed _item_type.code in _ihm_starting_model_coord.atom_id
;
0.121 2018-01-17
;
Changes (bv):
+ Added _ihm_derived_distance_restraint.distance_upper_limit_std and
_ihm_derived_distance_restraint.distance_lower_limit_std
+ Updated _item_type.code for _ihm_external_reference_info.reference_type and
_ihm_external_reference_info.reference_provider
;
0.122 2018-01-22
;
Changes (bv):
+ Updated parent-child relationships for _ihm_model_representation.entity_id,
_ihm_struct_assembly.entity_id, _ihm_feature_selection_atom.entity_id,
_ihm_feature_selection_residue.entity_id
+ Changed _ihm_derived_distance_restraint.distance_lower_limit_std to
_ihm_derived_distance_restraint.distance_lower_limit_esd
+ Changed _ihm_derived_distance_restraint.distance_upper_limit_std to
_ihm_derived_distance_restraint.distance_upper_limit_esd
+ Added enumeration for _ihm_external_reference_info.refers_to and
_ihm_external_files.file_format
;
0.123 2018-01-24
;
Changes (bv):
+ Added IHM_STRUCT_ASSEMBLY_DETAILS category.
+ Updated parent-child relationships for _ihm_starting_model_details.entity_description,
_ihm_model_representation.entity_description, _ihm_struct_assembly.entity_description,
_ihm_predicted_contact_restraint.entity_description_1, _ihm_cross_link_list.entity_description_1,
_ihm_predicted_contact_restraint.entity_description_2, _ihm_cross_link_list.entity_description_2
;
0.124 2018-02-01
;
Changes (bv):
+ Updated parent-child relationships for _ihm_model_representation.entity_id,
_ihm_struct_assembly.entity_id
+ Added IHM_FEATURE_LIST and IHM_NON_POLY_ATOM_FEATURE categories.
+ Changed IHM_FEATUTE_SELECTION_ATOM to IHM_POLY_ATOM_FEATURE.
+ Changed IHM_FEATUTE_SELECTION_RESDIUE to IHM_POLY_RESIDUE_FEATURE.
+ Updated IHM_DERIVED_DISTANCE_RESTRAINT
;
0.125 2018-02-05
;
Changes (bv):
+ Added _ihm_derived_distance_restraint.random_exclusion_fraction
+ Changed _ihm_derived_distance_restraint.conditionality to
_ihm_derived_distance_restraint.group_conditionality
+ Updated description for _ihm_derived_distance_restraint.group_conditionality
;
0.126 2018-02-06
;
Changes (bv):
+ Updated enumeration list for _ihm_dataset_list.data_type
;
0.127 2018-02-26
;
Changes (bv):
+ Added _ihm_poly_residue_feature.residue_range_granularity, _ihm_poly_residue_feature.rep_atom
+ Updated enumeration for _ihm_cross_link_list.linker_type, _ihm_external_files.content_type
;
0.128 2018-03-16
;
Changes (bv):
+ Added _ihm_dataset_group.application and _ihm_dataset_group.details
+ Updated enumeration for _ihm_modeling_post_process.type
+ Fixed typos
;
0.129 2018-03-22
;
Changes (bv):
+ Added _ihm_modeling_post_process.struct_assembly_id and _ihm_modeling_post_process.dataset_group_id
+ Added ihm_residues_not_modeled
;
0.130 2018-04-19
;
Changes (bv):
+ Updated enumeration for ihm_dataset_related_db_reference.db_name and ihm_dataset_list.data_type
;
0.131 2018-05-21
;
Changes (bv):
+ Added _ihm_modeling_post_process.software_id, _ihm_modeling_protocol.software_id
+ Added _ihm_multi_state_modeling.population_fraction_sd
+ Added _ihm_starting_comparative_models.software_id, _ihm_starting_comparative_models.script_file_id
+ Updated enumeration for _ihm_starting_model_details.starting_model_source
+ Updated _item.mandatory_code for _ihm_starting_comparative_models.starting_model_seq_id_begin
+ Updated _item.mandatory_code for _ihm_starting_comparative_models.starting_model_seq_id_end
;
0.132 2018-05-25
;
Changes (bv):
+ Added IHM_STARTING_COMPUTATIONAL_MODELS
+ Removed _ihm_starting_comparative_models.software_id, _ihm_starting_comparative_models.script_file_id
+ Added _ihm_modeling_post_process.script_file_id, _ihm_modeling_protocol.script_file_id
;
0.133 2018-06-29
;
Changes (bv):
+ Added IHM_GEOMETRIC_OBJECT_LIST, IHM_GEOMETRIC_OBJECT_CENTER, IHM_GEOMETRIC_OBJECT_TRANSFORMATION
+ Added IHM_GEOMETRIC_OBJECT_SPHERE, IHM_GEOMETRIC_OBJECT_TORUS, IHM_GEOMETRIC_OBJECT_HALF_TORUS
+ Added IHM_GEOMETRIC_OBJECT_AXIS, IHM_GEOMETRIC_OBJECT_PLANE, IHM_GEOMETRIC_OBJECT_DISTANCE_RESTRAINT
;
0.134 2018-07-18
;
Changes (bv):
+ Updated _item_sub_category.id for matrices and vectors
;
0.135 2018-10-04
;
Changes (bv):
+ Added DSSO crosslinker
+ Updated parent-child relationships for several data items:
_ihm_starting_model_details.entity_id, _ihm_model_representation.entity_id,
_ihm_struct_assembly.entity_id, _ihm_localization_density_files.entity_id,
_ihm_starting_model_coord.entity_id, _ihm_starting_model_coord.comp_id,
_ihm_sphere_obj_site.entity_id, _ihm_gaussian_obj_site.entity_id,
_ihm_gaussian_obj_ensemble.entity_id
+ Updated _item_type.code for _ihm_external_files.file_path
;
0.136 2018-10-05
;
Changes (bv):
+ Added ihm_hydroxyl_radical_fp_restraint
;
0.137 2018-10-26
;
Changes (bv):
+ Renamed IHM_NON_POLY_ATOM_FEATURE to IHM_NON_POLY_FEATURE
+ Updated _ihm_feature_list.feature_type
+ Added IHM_FEATURE_PSEUDO_SITE
;
0.138 2018-12-20
;
Changes (bv):
+ Added _ihm_modeling_protocol.ensemble_flag
+ Changed _item.type_code from code to ucode for:
_ihm_modeling_protocol.multi_scale_flag
_ihm_modeling_protocol.multi_state_flag
_ihm_modeling_protocol.ordered_flag
_ihm_dataset_list.database_hosted
_ihm_2dem_class_average_restraint.image_segment_flag
_ihm_3dem_restraint.map_segment_flag
_ihm_sas_restraint.profile_segment_flag
+ Updated definitions for _ihm_feature_list.entity_type
+ Updated enumeration list for _ihm_feature_list.feature_type
;
0.139 2019-01-03
;
Changes (bv):
+ Changed IHM_FEATURE_PSEUDO_SITE to IHM_PSEUDO_SITE_FEATURE
;
0.140 2019-03-11
;
Changes (bv):
+ Added IHM_INTERFACE_RESIDUE_FEATURE
+ Added _ihm_poly_residue_feature.interface_residue_flag
+ Updated item_mandatory.code for _ihm_poly_residue_feature.asym_id
_ihm_poly_atom_feature.asym_id, _ihm_non_poly_feature.asym_id
;
0.141 2019-05-06
;
Changes (bv):
+ Added IHM_CHEMICAL_COMPONENT_DESCRIPTOR, IHM_PROBE_LIST, IHM_EPR_RESTRAINT
+ Added IHM_POLY_PROBE_POSITION, IHM_POLY_PROBE_CONJUGATE
+ Added IHM_LIGAND_PROBE
+ Added _ihm_cross_link_list.linker_chem_comp_descriptor_id
;
1.0 2019-05-31
;
Changes (bv):
+ Updated several categories to fix primary key information and parent-child relationships
;
1.01 2019-07-26
;
Changes (bv):
+ Updated _item_mandatory.code and _pdbx_item.mandatory_code for several data items.
+ Added _item_sub_category.id in ihm_poly_probe_position.
+ Added PDB-Dev to the enumeration list in ihm_dataset_related_db_reference.db_name.
;
1.02 2019-10-01
;
Changes (bv):
+ Added _ihm_starting_model_details.description, _ihm_starting_comparative_models.details
+ Added _ihm_model_representation_details.description, _ihm_modeling_protocol_details.description
+ Added _ihm_modeling_post_process.details, _ihm_ensemble_info.details
+ Added _ihm_external_reference_info.details, _ihm_cross_link_list.details
+ Added _ihm_feature_list.details, _ihm_geometric_object_half_torus.details
+ Added enumerations (DSG and BSP) to _ihm_cross_link_list.linker_type
+ Updated _item_enumeration.detail for items in _ihm_cross_link_list.linker_type
+ Updated _item_description.description for _ihm_external_files.details
;
1.03 2019-10-03
;
Changes (bv):
+ Changed _ihm_geometric_object_distance_restraint.other_details to _ihm_geometric_object_distance_restraint.details
+ Removed _ihm_geometric_object_list.other_details and _ihm_geometric_object_half_torus.details
;
1.04 2019-10-10
;
Changes (bv):
+ Added _ihm_derived_distance_restraint.mic_value
+ Added enumeration to _ihm_dataset_list.data_type
;
1.05 2019-11-15
;
Changes (bv):
+ Added BMSO and DHSO to _ihm_cross_link_list.linker_type enumeration list
;
1.06 2020-01-24
;
Changes (bv):
+ Added _ihm_cross_link_restraint.pseudo_site_flag
+ Added ihm_cross_link_pseudo_site category
+ Added ihm_pseudo_site category
+ Removed _ihm_pseudo_site_feature.Cartn_x, _ihm_pseudo_site_feature.Cartn_y
_ihm_pseudo_site_feature.Cartn_z, _ihm_pseudo_site_feature.radius
_ihm_pseudo_site_feature.description
+ Added _ihm_pseudo_site_feature.pseudo_site_id
;
1.07 2020-02-10
;
Changes (bv):
+ Added CYS to _ihm_cross_link_list.linker_type enumeration list
;
1.08 2020-02-14
;
Changes (bv):
+ Added _ihm_ensemble_info.sub_sample_flag, _ihm_ensemble_info.sub_sampling_type
+ Added ihm_ensemble_sub_sample
;
1.09 2020-03-19
;
Changes (bv):
+ Added ihm_data_transformation
+ Added _ihm_related_datasets.transformation_id
;
1.10 2020-06-04
;
Changes (bv):
+ Added ihm_derived_angle_restraint, ihm_derived_dihedral_restraint
+ Added _ihm_derived_distance_restraint.distance_threshold_mean
+ Added _ihm_derived_distance_restraint.distance_threshold_esd
+ Updated enumeration for _ihm_derived_distance_restraint.restraint_type
+ Updated enumeration for _ihm_dataset_list.data_type
;
1.11 2020-07-03
;
Changes (bv):
+ Added ihm_hdx_restraint
;
1.12 2020-07-10
;
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
;
1.13 2021-01-28
;
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
;
1.14 2021-03-04
;
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
;
1.15 2021-03-16
;
Changes (bv):
+ Added enumerations to _ihm_dataset_related_db_reference.db_name
;
1.16 2021-04-14
;
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
;
1.17 2021-05-21
;
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
;
1.18 2022-12-20
;
Changes (bv):
+ Added _ihm_ensemble_info.model_group_superimposed_flag
+ Added enumerations to _ihm_dataset_list.data_type and _ihm_ensemble_info.ensemble_clustering_method
+ Added ihm_entry_collection and ihm_entry_collection_mapping
;
1.19 2023-02-02
;
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type and _ihm_dataset_related_db_reference.db_name
;
1.20 2023-02-19
;
Changes (bv):
+ Updated category keys for ihm_entry_collection_mapping
+ Added enumerations to _ihm_cross_link_list.linker_type and _ihm_dataset_related_db_reference.db_name
+ Add nanoseconds to item_units_list
;
1.21 2023-03-24
;
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
;
1.22 2023-05-26
;
Changes (bv):
+ Added enumerations to _ihm_dataset_related_db_reference.db_name
;
1.23 2023-07-05
;
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
;
1.24 2023-11-30
;
Changes (bv):
+ Added ihm_multi_state_scheme, ihm_multi_state_scheme_connectivity
+ Added ihm_kinetic_rate, ihm_relaxation_time, ihm_relaxation_time_multi_state_scheme
;
1.25 2023-12-22
;
+ Rename dictionary
+ Reorganize repository
;
1.26 2024-07-11
;
+ Add "Crosslinking-MS" to the enumeration list of _ihm_dataset_list.data_type
+ Add "modeling" to the enumeration list of _ihm_dataset_group.application
+ Update category descriptions of ihm_model_list, ihm_model_group, ihm_model_group_link, ihm_model_representative
+ Add category "ihm_ordered_model" and deprecate category "ihm_ordered_ensemble"
+ Update enumerations for _ihm_cross_link_list.linker_type
+ Update _item_type.code for _ihm_dataset_related_db_reference.accession_code and _ihm_ensemble_info.ensemble_clustering_method
+ Add "ProteomeXchange" to the enumeration list of _ihm_dataset_related_db_reference.db_name
;
1.27 2024-11-25
;
+ Added BMRbig to the enumeration list in ihm_dataset_related_db_reference.db_name
;
#
loop_
_pdbx_dictionary_component.datablock_id
_pdbx_dictionary_component.dictionary_component_id
_pdbx_dictionary_component.title
_pdbx_dictionary_component.version
mmcif_ihm-data.dic mmcif_ihm-data.dic "IHMCIF dictionary: mmcif_ihm-data" 1.0
entity_poly_seq.dic entity_poly_seq.dic "entity_poly_seq for IHMCIF" 0.001
mmcif_ihm-core.dic mmcif_ihm-core.dic "IHMCIF dictionary: mmcif_ihm-core" 1.27
#
loop_
_pdbx_dictionary_component_history.dictionary_component_id
_pdbx_dictionary_component_history.version
_pdbx_dictionary_component_history.update
_pdbx_dictionary_component_history.revision
mmcif_ihm-data.dic 1.0 2023-12-22
;
Changes (bv)
+ Updated dictionary files organization
;
entity_poly_seq.dic 0.001 2023-12-22
;
Changes (bv)
+ Release as initial version 0.001
;
mmcif_ihm-core.dic 0.000 2017-03-20
;
Changes (jdw/bv)
+ Release as initial version 0.000
+ Changed _imp to _ihm
+ Changed _imp_template_details to _ihm_starting_model_details
+ Changed _imp_tempate_model_coord to _ihm_starting_model_coord
+ Changed _imp_pseudo_atom_site to _ihm_sphere_object_site
+ Added enumeration 'integrative' to _ihm_starting_model_details.starting_model_source
+ Separated ihm_cross_link_restraint and ihm_cross_link_list categories
+ Updated ambiguous crosslinks in ihm_cross_link_restraint and ihm_cross_link_list categories
+ Added ihm_dataset_list, ihm_related_database_reference and ihm_dataset_other categories
+ Added ihm_cross_link_result (yet to be completed) and ihm_entity_assembly categories
+ Updated ihm_2dem_class_average_restraint category
+ Removed ihm_cross_link_db_reference, ihm_cross_link_reference_auxiliary, ihm_2dem_class_average categories
+ Revised several data items to be non-mandatory
+ Changed category key item in ihm_model_details category to account for multiple coarse-grained representations
of the same model segment (introduced _ihm_model_details.ordinal_id)
+ Updated _ihm_sphere_obj_site.entity_instance_id, ihm_cross_link_restraint (psi and sigma parameters)
+ Added ihm_modeling_protocol, ihm_cluster_info, ihm_struct_assembly (previously ihm_entity_assembly)
+ Added _ihm_3dem_restraint category; minor changes to other categories
+ Changed ihm_model_details category name to ihm_model_representation (handles multi-scale representation)
+ Changed several data items in the ihm_modeling_protocol category
+ Added ihm_modeling_post_process, ihm_model_list, ihm_multi_state_modeling,
ihm_time_ordered_ensemble, ihm_gaussian_object_site categories
+ Linked ihm_model_list to ihm_sphere_obj_site through model_id
+ Linked ihm_starting_model_details to ihm_dataset_list through dataset_list_id
+ Added new data item _ihm_model_representation.representation_id and more changes to ihm_modeling_protocol
and ihm_gaussian_obj_site categories.
+ Added ihm_gaussian_obj_ensemble category to represent ensembles as gaussian objects - to be different from
+ ihm_gaussian_object_site category that is used in model representation and hence by visualization software.
+ Changed ihm_cluster_info category name to ihm_ensemble_info and changed relevant data item names accordingly.
+ Changed ihm_related_database_reference category name to ihm_dataset_related_db_reference to be consistent
with other similar categories
+ Minor changes in other categories: ihm_model_list, ihm_dataset_list, ihm_modeling_protocol, ihm_ensemble_info,
ihm_multi_state_modeling, ihm_time_ordered_ensemble, ihm_2dem_class_average_restraint (data items are now
similar to 2D class average images in EMPIAR), ihm_model_represenation.
+ Updated parent-child relationships across several categories (ihm_modeling_protocol, ihm_ensemble_info
ihm_model_list, ihm_multi_state_modeling, ihm_time_ordered_ensemble, ihm_2dem_class_average_fitting,
ihm_cross_link_result)
+ Updated examples in ihm_dataset_list, ihm_dataset_other and ihm_dataset_related_db_reference
+ Changed ihm_modeling_experiment to ihm_modeling_protocol to be consistent with the model archive naming convention
+ Added ihm_sas_restraint category; added _ihm_3dem_restraint.map_segment_flag
+ Modified the following categories: ihm_model_list, ihm_modeling_protocol, ihm_multi_state_modeling,
ihm_time_ordered_ensemble
+ Minor updates to ihm_cross_link_list, ihm_cross_link_restraint and ihm_model_representation categories.
+ Added _ihm_sphere_obj_site.rmsf and _ihm_starting_model_details.asym_id
+ Added ihm_related_datasets and ihm_cross_link_result_parameters
+ Added _ihm_3dem_restraint.struct_assembly_id, _ihm_sas_restraint.struct_assembly_id,
_ihm_starting_model_details.notes and _ihm_starting_model_coord.group_PDB
+ Changed _ihm_3dem_restraint.id to _ihm_3dem_restraint.ordinal_id and _ihm_sas_restraint.id to
_ihm_sas_restraint.ordinal_id
+ Changed _ihm_dataset_related_db_reference.access_code to _ihm_dataset_related_db_reference.accession_code
+ Added new categories to reference externally hosted files: IHM_LOCALIZATION_DENSITY_FILES,
+ IHM_STARTING_MODEL_ALIGNMENT_FILES, IHM_MODELING_WORKFLOW_FILES
+ Added IHM_DATA_DOI_URL_INFO category to include a URL corresponding to a DOI. This enables automated
download of files.
+ Removed redundant DOI references from several categories
+ Added _ihm_starting_model_details.starting_model_sequence_offset
+ Changed _ihm_starting_model_details.starting_model_db_pdb_auth_asym_id to
_ihm_starting_model_details.starting_model_auth_asym_id
+ Changed IHM_DOI_URL_INFO to IHM_EXTERNAL_REFERENCE_INFO; modified all downstream dependencies
+ Changed IHM_DATASET_OTHER to IHM_DATASET_EXTERNAL_REFERENCE_DETAILS; modified all downstream dependencies
+ Modified definitions within IHM_EXTERNAL_REFERENCE_INFO
+ Added IHM_EXTERNAL_FILES category; Removed IHM_STARTING_MODEL_ALIGNMENT_FILES category
+ Changed IHM_MODELING_WORKFLOW_FILES, IHM_LOCALIZATION_DENSITY_FILES
+ Changed IHM_DATASET_EXTERNAL_REFERENCE_DETAILS to IHM_DATASET_EXTERNAL_REFERENCE
+ Modified IHM_STARTING_MODEL_DETAILS category
+ Added IHM_STARTING_COMPARATIVE_MODELS category
+ Added IHM_STARTING_MODEL_SEQ_DIF category; removed _ihm_starting_model_details.notes
+ Updated IHM_ENSEMBLE_INFO, IHM_EXTERNAL_FILES and IHM_EXTERNAL_REFERENCE_INFO
+ Added _ihm_multi_state_modeling.experiment_type; updated IHM_ENSEMBLE_INFO
;
mmcif_ihm-core.dic 0.100 2017-03-23
;
Changes (bv):
+ Release as provisional version 0.100
+ Added _ihm_external_files.content_type
+ Added _ihm_external_files.details
+ Removed IHM_MODELING_WORKFLOW_FILES
;
mmcif_ihm-core.dic 0.101 2017-03-29
;
Changes (bv):
+ Updated _ihm_starting_model_seq_dif.db_entity_id as non-mandatory
;
mmcif_ihm-core.dic 0.102 2017-03-29
;
Changes (bv):
+ Updated examples in IHM_STARTING_COMPARATIVE_MODELS
;
mmcif_ihm-core.dic 0.103 2017-03-30
;
Changes (bv):
+ Updated IHM_STARTING_MODEL_DETAILS
+ Updated IHM_STARTING_COMPARATIVE_MODELS
+ Updated IHM_DATASET_LIST, IHM_RELATED_DATASETS
+ Updated IHM_DATASET_RELATED_DB_REFERENCE
+ Updated IHM_DATASET_EXTERNAL_REFERENCE
+ Added examples to IHM_EXTERNAL_REFERENCE_INFO and IHM_EXTERNAL_FILES
;
mmcif_ihm-core.dic 0.104 2017-04-19
;
Changes (bv):
+ Updated IHM_STARTING_MODEL_DETAILS
+ Updated IHM_STARTING_COMPARATIVE_MODELS
+ Updated IHM_STARTING_MODEL_SEQ_DIF
+ Updated IHM_MODEL_REPRESENTATION
+ Updated IHM_DATASET_LIST
+ Added IHM_DATASET_GROUP
+ Updated IHM_MODELING_PROTOCOL
;
mmcif_ihm-core.dic 0.105 2017-05-25
;
Changes (bv):
+ Added item description to _ihm_ensemble_info.ensemble_file_id
+ Added item description to _ihm_2dem_class_average_restraint.pixel_size_width
+ Added item description to _ihm_2dem_class_average_restraint.pixel_size_height
+ Added category description to ihm_2dem_class_average_fitting
+ Added enumeration 'DCD' to _ihm_external_files.file_format
+ Changed _ihm_external_files.file_size_kb to _ihm_external_files.file_size_bytes
;
mmcif_ihm-core.dic 0.106 2017-07-13
;
Changes (bv):
+ Updated dictionary description and version history
;
mmcif_ihm-core.dic 0.107 2017-07-17
;
Changes (ep/bv):
+ Added category_group_list, item_type_list and item_units_list categories
;
mmcif_ihm-core.dic 0.108 2017-09-12
;
Changes (bv):
+ Added IHM_STRUCT_ASSEMBLY_CLASS, IHM_STRUCT_ASSEMBLY_CLASS_LIST
+ Added _ihm_struct_assembly.parent_assembly_id
;
mmcif_ihm-core.dic 0.109 2017-09-28
;
Changes (bv):
+ Added _ihm_model_list.representation_id
+ Added _atom_site.ihm_model_id
;
mmcif_ihm-core.dic 0.110 2017-10-03
;
Changes (bv):
+ Added _ihm_cross_link_restraint.atom_id_1, _ihm_cross_link_restraint.atom_id_2
+ Added _ihm_cross_link_restraint.restraint_type
+ Changed _ihm_cross_link_restraint.type to _ihm_cross_link_restraint.linker_type
+ Changed _ihm_cross_link_list.type to _ihm_cross_link_list.linker_type
+ Added enumerations to _ihm_cross_link_restraint.linker_type and _ihm_cross_link_list.linker_type
+ Added enumeration to and changed _item.mandatory_code of _ihm_cross_link_restraint.model_granularity
+ Added ihm_predicted_contact_restraint category
+ Added enumeration to _ihm_dataset_list.data_type
;
mmcif_ihm-core.dic 0.111 2017-10-04
;
Changes (bv):
+ Removed _ihm_cross_link_restraint.linker_type
+ Updated enumerations to _ihm_cross_link_restraint.restraint_type
;
mmcif_ihm-core.dic 0.112 2017-10-04
;
Changes (bv):
+ Added _ihm_dataset_list.details
+ Added enumeration to _ihm_dataset_list.data_type
;
mmcif_ihm-core.dic 0.113 2017-10-06
;
Changes (bv):
+ Added IHM_MODEL_REPRESENTATIVE
+ Added enumeration to _ihm_cross_link_list.linker_type
+ Updated item description for _ihm_predicted_contact_restraint.probability
;
mmcif_ihm-core.dic 0.114 2017-10-09
;
Changes (bv):
+ Fixed typos and syntax
;
mmcif_ihm-core.dic 0.115 2017-10-12
;
Changes (bv):
+ Added _ihm_modeling_post_process.feature_name
+ Fixed enumeration for _ihm_cross_link_list.linker_type
;
mmcif_ihm-core.dic 0.116 2017-10-16
;
Changes (bv):
+ Updated _item_description.description for _ihm_model_list.model_group_id
+ Updated enumerations for _ihm_dataset_list.data_type
+ Updated parent-child relationships within _ihm_model_list.model_id
;
mmcif_ihm-core.dic 0.117 2017-11-09
;
Changes (bv):
+ Updated description for _ihm_starting_model_details.starting_model_sequence_offset
;
mmcif_ihm-core.dic 0.118 2017-12-06
;
Changes (bv):
+ Changed ihm_time_ordered_ensemble to ihm_ordered_ensemble with appropriate revisions to the category
+ Changed _ihm_modeling_protocol.time_ordered_flag to _ihm_modeling_protocol.ordered_flag
+ Changed mandatory code for _ihm_model_list.representation_id
+ Added an example to ihm_model_list category
;
mmcif_ihm-core.dic 0.119 2017-12-07
;
Changes (bv):
+ Changed ihm_ordered_ensemble.ordered_process_id to ihm_ordered_ensemble.process_id
+ Changed ihm_ordered_ensemble.ordered_process_description to ihm_ordered_ensemble.process_description.
+ Changed parent-child relationships for _ihm_predicted_contact_restraint.atom_id_1,
_ihm_predicted_contact_restraint.atom_id_2, _ihm_cross_link_restraint.atom_id_1,
_ihm_cross_link_restraint.atom_id_2, _ihm_starting_model_coord.atom_id
;
mmcif_ihm-core.dic 0.120 2018-01-10
;
Changes (bv):
+ Added ihm_feature_selection_atom, ihm_feature_selection_residue, ihm_derived_distance_restraint
+ Fixed typos in the parent name of _ihm_predicted_contact_restraint.atom_id_1 and
_ihm_predicted_contact_restraint.atom_id_2
+ Fixed _item_type.code in _ihm_starting_model_coord.atom_id
;
mmcif_ihm-core.dic 0.121 2018-01-17
;
Changes (bv):
+ Added _ihm_derived_distance_restraint.distance_upper_limit_std and
_ihm_derived_distance_restraint.distance_lower_limit_std
+ Updated _item_type.code for _ihm_external_reference_info.reference_type and
_ihm_external_reference_info.reference_provider
;
mmcif_ihm-core.dic 0.122 2018-01-22
;
Changes (bv):
+ Updated parent-child relationships for _ihm_model_representation.entity_id,
_ihm_struct_assembly.entity_id, _ihm_feature_selection_atom.entity_id,
_ihm_feature_selection_residue.entity_id
+ Changed _ihm_derived_distance_restraint.distance_lower_limit_std to
_ihm_derived_distance_restraint.distance_lower_limit_esd
+ Changed _ihm_derived_distance_restraint.distance_upper_limit_std to
_ihm_derived_distance_restraint.distance_upper_limit_esd
+ Added enumeration for _ihm_external_reference_info.refers_to and
_ihm_external_files.file_format
;
mmcif_ihm-core.dic 0.123 2018-01-24
;
Changes (bv):
+ Added IHM_STRUCT_ASSEMBLY_DETAILS category.
+ Updated parent-child relationships for _ihm_starting_model_details.entity_description,
_ihm_model_representation.entity_description, _ihm_struct_assembly.entity_description,
_ihm_predicted_contact_restraint.entity_description_1, _ihm_cross_link_list.entity_description_1,
_ihm_predicted_contact_restraint.entity_description_2, _ihm_cross_link_list.entity_description_2
;
mmcif_ihm-core.dic 0.124 2018-02-01
;
Changes (bv):
+ Updated parent-child relationships for _ihm_model_representation.entity_id,
_ihm_struct_assembly.entity_id
+ Added IHM_FEATURE_LIST and IHM_NON_POLY_ATOM_FEATURE categories.
+ Changed IHM_FEATUTE_SELECTION_ATOM to IHM_POLY_ATOM_FEATURE.
+ Changed IHM_FEATUTE_SELECTION_RESDIUE to IHM_POLY_RESIDUE_FEATURE.
+ Updated IHM_DERIVED_DISTANCE_RESTRAINT
;
mmcif_ihm-core.dic 0.125 2018-02-05
;
Changes (bv):
+ Added _ihm_derived_distance_restraint.random_exclusion_fraction
+ Changed _ihm_derived_distance_restraint.conditionality to
_ihm_derived_distance_restraint.group_conditionality
+ Updated description for _ihm_derived_distance_restraint.group_conditionality
;
mmcif_ihm-core.dic 0.126 2018-02-06
;
Changes (bv):
+ Updated enumeration list for _ihm_dataset_list.data_type
;
mmcif_ihm-core.dic 0.127 2018-02-26
;
Changes (bv):
+ Added _ihm_poly_residue_feature.residue_range_granularity, _ihm_poly_residue_feature.rep_atom
+ Updated enumeration for _ihm_cross_link_list.linker_type, _ihm_external_files.content_type
;
mmcif_ihm-core.dic 0.128 2018-03-16
;
Changes (bv):
+ Added _ihm_dataset_group.application and _ihm_dataset_group.details
+ Updated enumeration for _ihm_modeling_post_process.type
+ Fixed typos
;