Supporting Data mmcif_ihm_ext.dic

Dictionary Revision History

Version Revision Date Revision Description
1.25 2023-12-22
+ Rename dictionary
+ Reorganize repository
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
1.23 2023-07-05
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
mmcif_ihm_ext.dic
1.22 2023-05-26
Changes (bv):
+ Added enumerations to _ihm_dataset_related_db_reference.db_name
mmcif_ihm_ext.dic
1.21 2023-03-24
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
1.19 2023-02-02
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type and _ihm_dataset_related_db_reference.db_name
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
1.17 2021-05-21
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
mmcif_ihm_ext.dic
1.16 2021-04-14
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
mmcif_ihm_ext.dic
1.15 2021-03-16
Changes (bv):
+ Added enumerations to _ihm_dataset_related_db_reference.db_name
mmcif_ihm_ext.dic
1.14 2021-03-04
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
mmcif_ihm_ext.dic
1.13 2021-01-28
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
mmcif_ihm_ext.dic
1.12 2020-07-10
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
mmcif_ihm_ext.dic
1.11 2020-07-03
Changes (bv):
+ Added ihm_hdx_restraint
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
1.09 2020-03-19
Changes (bv):
+ Added ihm_data_transformation
+ Added _ihm_related_datasets.transformation_id
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
1.07 2020-02-10
Changes (bv):
+ Added CYS to _ihm_cross_link_list.linker_type enumeration list
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
1.05 2019-11-15
Changes (bv):
+ Added BMSO and DHSO to _ihm_cross_link_list.linker_type enumeration list
mmcif_ihm_ext.dic
1.04 2019-10-10
Changes (bv):
+ Added _ihm_derived_distance_restraint.mic_value
+ Added enumeration to _ihm_dataset_list.data_type
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
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.
mmcif_ihm_ext.dic
1.0 2019-05-31
Changes (bv):
+ Updated several categories to fix primary key information and parent-child relationships
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
0.139 2019-01-03
Changes (bv):
+ Changed IHM_FEATURE_PSEUDO_SITE to IHM_PSEUDO_SITE_FEATURE
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
0.136 2018-10-05
Changes (bv):
+ Added ihm_hydroxyl_radical_fp_restraint
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
0.134 2018-07-18
Changes (bv):
+ Updated _item_sub_category.id for matrices and vectors
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
0.130 2018-04-19
Changes (bv):
+ Updated enumeration for ihm_dataset_related_db_reference.db_name and ihm_dataset_list.data_type
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.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
mmcif_ihm_ext.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_ext.dic
0.126 2018-02-06
Changes (bv):
+ Updated enumeration list for _ihm_dataset_list.data_type
mmcif_ihm_ext.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_ext.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_ext.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_ext.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_ext.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_ext.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_ext.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_ext.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_ext.dic
0.117 2017-11-09
Changes (bv):
+ Updated description for _ihm_starting_model_details.starting_model_sequence_offset
mmcif_ihm_ext.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_ext.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_ext.dic
0.114 2017-10-09
Changes (bv):
+ Fixed typos and syntax
mmcif_ihm_ext.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_ext.dic
0.112 2017-10-04
Changes (bv):
+ Added _ihm_dataset_list.details
+ Added enumeration to _ihm_dataset_list.data_type
mmcif_ihm_ext.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_ext.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_ext.dic
0.109 2017-09-28
Changes (bv):
+ Added _ihm_model_list.representation_id
+ Added _atom_site.ihm_model_id
mmcif_ihm_ext.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_ext.dic
0.107 2017-07-17
Changes (ep/bv):
+ Added category_group_list, item_type_list and item_units_list categories
mmcif_ihm_ext.dic
0.106 2017-07-13
Changes (bv):
+ Updated dictionary description and version history
mmcif_ihm_ext.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_ext.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_ext.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_ext.dic
0.102 2017-03-29
Changes (bv):
+ Updated examples in IHM_STARTING_COMPARATIVE_MODELS
mmcif_ihm_ext.dic
0.101 2017-03-29
Changes (bv):
+ Updated _ihm_starting_model_seq_dif.db_entity_id as non-mandatory
mmcif_ihm_ext.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_ext.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_ext.dic
1.25 2023-12-22
+ Rename dictionary
+ Reorganize repository
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
1.23 2023-07-05
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
mmcif_ihm_ext.dic
1.22 2023-05-26
Changes (bv):
+ Added enumerations to _ihm_dataset_related_db_reference.db_name
mmcif_ihm_ext.dic
1.21 2023-03-24
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
1.19 2023-02-02
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type and _ihm_dataset_related_db_reference.db_name
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
1.17 2021-05-21
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
mmcif_ihm_ext.dic
1.16 2021-04-14
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
mmcif_ihm_ext.dic
1.15 2021-03-16
Changes (bv):
+ Added enumerations to _ihm_dataset_related_db_reference.db_name
mmcif_ihm_ext.dic
1.14 2021-03-04
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
mmcif_ihm_ext.dic
1.13 2021-01-28
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
mmcif_ihm_ext.dic
1.12 2020-07-10
Changes (bv):
+ Added enumerations to _ihm_cross_link_list.linker_type
mmcif_ihm_ext.dic
1.11 2020-07-03
Changes (bv):
+ Added ihm_hdx_restraint
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
1.09 2020-03-19
Changes (bv):
+ Added ihm_data_transformation
+ Added _ihm_related_datasets.transformation_id
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
1.07 2020-02-10
Changes (bv):
+ Added CYS to _ihm_cross_link_list.linker_type enumeration list
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
1.05 2019-11-15
Changes (bv):
+ Added BMSO and DHSO to _ihm_cross_link_list.linker_type enumeration list
mmcif_ihm_ext.dic
1.04 2019-10-10
Changes (bv):
+ Added _ihm_derived_distance_restraint.mic_value
+ Added enumeration to _ihm_dataset_list.data_type
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
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.
mmcif_ihm_ext.dic
1.0 2019-05-31
Changes (bv):
+ Updated several categories to fix primary key information and parent-child relationships
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
0.139 2019-01-03
Changes (bv):
+ Changed IHM_FEATURE_PSEUDO_SITE to IHM_PSEUDO_SITE_FEATURE
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
0.136 2018-10-05
Changes (bv):
+ Added ihm_hydroxyl_radical_fp_restraint
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
0.134 2018-07-18
Changes (bv):
+ Updated _item_sub_category.id for matrices and vectors
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.dic
0.130 2018-04-19
Changes (bv):
+ Updated enumeration for ihm_dataset_related_db_reference.db_name and ihm_dataset_list.data_type
mmcif_ihm_ext.dic
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
mmcif_ihm_ext.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
mmcif_ihm_ext.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_ext.dic
0.126 2018-02-06
Changes (bv):
+ Updated enumeration list for _ihm_dataset_list.data_type
mmcif_ihm_ext.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_ext.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_ext.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_ext.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_ext.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_ext.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_ext.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_ext.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_ext.dic
0.117 2017-11-09
Changes (bv):
+ Updated description for _ihm_starting_model_details.starting_model_sequence_offset
mmcif_ihm_ext.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_ext.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_ext.dic
0.114 2017-10-09
Changes (bv):
+ Fixed typos and syntax
mmcif_ihm_ext.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_ext.dic
0.112 2017-10-04
Changes (bv):
+ Added _ihm_dataset_list.details
+ Added enumeration to _ihm_dataset_list.data_type
mmcif_ihm_ext.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_ext.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_ext.dic
0.109 2017-09-28
Changes (bv):
+ Added _ihm_model_list.representation_id
+ Added _atom_site.ihm_model_id
mmcif_ihm_ext.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_ext.dic
0.107 2017-07-17
Changes (ep/bv):
+ Added category_group_list, item_type_list and item_units_list categories
mmcif_ihm_ext.dic
0.106 2017-07-13
Changes (bv):
+ Updated dictionary description and version history
mmcif_ihm_ext.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_ext.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_ext.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_ext.dic
0.102 2017-03-29
Changes (bv):
+ Updated examples in IHM_STARTING_COMPARATIVE_MODELS
mmcif_ihm_ext.dic
0.101 2017-03-29
Changes (bv):
+ Updated _ihm_starting_model_seq_dif.db_entity_id as non-mandatory
mmcif_ihm_ext.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_ext.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_ext.dic
Data Type Code Primitive Type Code Regular Expression Description
3x4_matrices char (((([ \t]*-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? +){3})?(-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? *\n([\t ]*\n)*)){3})*((([ \t]*-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? +){3})?(-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? *\n([\t ]*\n)*)){2}((([ \t]*-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? +){3})(-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? *\n?([\t ]*\n)*))[ \t]* A set of 3x4 matrices separated by spaces and newlines on each line.
Final newline optional. Optional spaces at start of lines. Blank lines accepted.
3x4_matrix char ((([ \t]*-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? +){3})?(-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? *\n([\t ]*\n)*)){2}((([ \t]*-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? +){3})(-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? *\n?([\t ]*\n)*))[ \t]* A 3x4 matrix separated by spaces and newlines on each line.
Final newline optional. Optional spaces at start of lines. Blank lines accepted.
any char .* A catch all for items that may take any form...
asym_id char [A-Za-z0-9]+ A single chain or asym ids.
atcode char [][ _(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* Character data type for atom names ...
author char (([A-Za-z0-9_]+(( |-|'|\. )[A-Za-z0-9_]+)*( Jr.| III)?, [A-Za-z0-9_]\.(-?[A-Za-z0-9_]+\.)*)|(Seattle Structural Genomics Center for Infectious Disease.*)|(Structural Genomics Consortium.*)|(QCRG Structural Biology Consortium.*)|(Center for Structural Genomics of Infectious Diseases.*)) Author name in PDB format: Taylor, C.A.
binary char \n--CIF-BINARY-FORMAT-SECTION--\n\
[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*\
\n--CIF-BINARY-FORMAT-SECTION----
binary items are presented as MIME-like ascii-encoded
sections in an imgCIF. In a CBF, raw octet streams
are used to convey the same information.
boolean char YES|NO Boolean type
citation_doi char 10\..* Citation DOI specification.
code char [][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words ...
code30 char .?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.? A string value, not allowed to exceed 30 characters.
date_dep char ([1-9][0-9](([02468][048])|([13579][26]))-02-29)|[1-9][0-9][0-9][0-9]-((((0[1-9])|(1[0-2]))-((0[1-9])|(1[0-9])|(2[0-8])))|((((0[13578])|(1[02]))-31)|(((0[1,3-9])|(1[0-2]))-(29|30)))) Deposition specific date with better checking
deposition_email uchar [a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9.-]+ code item types/single words (case insensitive) ...
ec-type char ([1-7]((.[1-9][0-9]?)|(.-))((.[1-9][0-9]?)|(.-))((.[1-9][0-9]?[0-9]?)|(.-)))(([ ]*,[ ]*)([1-7]((.[1-9][0-9]?)|(.-))((.[1-9][0-9]?)|(.-))((.[1-9][0-9]?[0-9]?)|(.-))))*
Approximate format of Enzyme Commission EC number. 1.2.3.4 with
optional parts.
email uchar [_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words (case insensitive) ...
emd_id char EMD-[0-9]{4,} EMDB code
exp_data_doi char 10\.[0-9]{4,9}/[-._;()/:A-Za-z0-9]+ Experimental dataset DOI
fax uchar [_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words (case insensitive) ...
float numb -?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? float item types are the subset of numbers that are the floating
numbers.
float-range numb -?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?(--?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?)? int item types are the subset of numbers that are the floating
numbers.
id_list char [A-Za-z0-9]+(,[A-Za-z0-9]+)* A list of comma separated chain or asym ids.
id_list_spc char [ \t]*[A-Za-z0-9]+([ \t]*,[ \t]*[A-Za-z0-9]+)*[ \t]* A list of comma separated chain or asym ids with optional spaces.
idname uchar [_A-Za-z0-9]+ idname item types take the form...
int numb [+-]?[0-9]+ int item types are the subset of numbers that are the negative
or positive integers.
int-range numb [+-]?[0-9]+-[+-]?[0-9]+ range of integer item types are the subset of numbers that are the negative
or positive integers.
line char [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* char item types / multi-word items ...
name uchar _[_A-Za-z0-9]+\.[][_A-Za-z0-9%-]+ name item types take the form...
operation_expression char [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* sequence of parenthetical integer ranges and character codes
orcid_id char [0-9]{4}-[0-9]{4}-[0-9]{4}-([0-9]{3}X|[0-9]{4}) ORCID pattern - dddd-dddd-dddd-dddd|dddX
pdb_id char ([1-9][A-Z0-9]{3}|PDB_[A-Z0-9]{8}) PDB code (upper cases)
pdb_id_u uchar ([1-9][A-Za-z0-9]{3}|[Pp][Dd][Bb]_[A-Za-z0-9]{8}) PDB code (case insensitive)
pdbx_PDB_obsoleted_db_id char [0-9][0-9a-zA-Z]{3}( [0-9][0-9a-zA-Z]{3})* List of PDB ids for obsoletion - space separated
pdbx_related_db_id char [][_.:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words without semi-colon or comma ...
phone uchar [_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words (case insensitive) ...
point_group char (C[1-9][0-9]*|D[2-9]|D[1-9][0-9]+|O|T|I) Point group symmetry in Schoenflies notation
point_group_helical char [CD][1-9][0-9]* Point group symmetry for helices in Schoenflies notation
point_symmetry char [CD][1-9]|[CD][1-9][0-9]*|T|O|I Encodes point symmetry as Cn, Dn, T, O, or I (case sensitive), where n is a positive integer.
positive_int numb [1-9][0-9]* Positive integers (1,2,3,..)
seq-one-letter-code char (([\nUGPAVLIMCFYWHKRQNEDSTX]+)?|(\([0-9A-Z][0-9A-Z]?[0-9A-Z]?\))?)+ One letter code sequence supporting parenthetical modified residues with 3-letter codes
sequence_dep char [a-zA-Z0-9\t \r\n\v\f\(\)]+$ Deposition specific one letter code
symmetry_operation char [-+0-9XxYyZ/ ]+,[-+0-9XxYyZ/ ]+,[-+0-9XxYyZ/ ]+ Allowed characters for use in symmetry operation such as 1/2-x,y,1/2-z
symop char ([1-9]|[1-9][0-9]|1[0-8][0-9]|19[0-2])(_[1-9][1-9][1-9])? symop item types take the form n_klm, where n refers to the
symmetry operation that is applied to the coordinates in the
ATOM_SITE category identified by _atom_site_label. It must
match a number given in _symmetry_equiv_pos_site_id.

k, l, and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used. These translations (x,y,z) are related to
(k,l,m) by
k = 5 + x
l = 5 + y
m = 5 + z
By adding 5 to the translations, the use of negative numbers
is avoided.
text char [][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* text item types / multi-line text ...
uchar1 uchar [+]?[A-Za-z0-9]
data item for 1 character codes
uchar3 uchar [+]?[A-Za-z0-9][A-Za-z0-9]?[A-Za-z0-9]?
data item for 3 character codes
uchar5 uchar [+]?[A-Za-z0-9][A-Za-z0-9]?[A-Za-z0-9]?[A-Za-z0-9]?[A-Za-z0-9]?
data item for 5 character codes
ucode uchar [][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words (case insensitive) ...
ucode-alphanum-csv uchar [A-Za-z0-9]+(,[A-Za-z0-9]+)? comma separated alpha numeric codes (single words) (case insensitive) ...
uline uchar [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* char item types / multi-word items (case insensitive)...
yyyy-mm-dd char [0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]
Standard format for CIF dates.
yyyy-mm-dd:hh:mm char [0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9](-[0-9]?[0-9])?(:[0-9]?[0-9]:[0-9][0-9])?
Standard format for CIF dates with optional time stamp.
yyyy-mm-dd:hh:mm-flex char [0-9][0-9][0-9][0-9](-[0-9]?[0-9])?(-[0-9][0-9])?(:[0-9]?[0-9]:[0-9][0-9])?
Flexible date-time format.
SubCategory Identifier Description
cartesian_coordinate The collection of x, y, and z components of a position specified
with reference to a Cartesian (orthogonal angstrom) coordinate
system.
cartesian_coordinate_esd The collection of estimated standard deviations of the x, y, and
z components of a position specified with reference to a
Cartesian (orthogonal angstrom) coordinate system.
cell_angle The collection of alpha, beta, and gamma angles of a unit cell.
cell_angle_esd The collection of estimated standard deviations of the alpha,
beta, and gamma angles of a unit cell.
cell_length The collection of a, b, and c axis lengths of a unit cell.
cell_length_esd The collection of estimated standard deviations of the a, b, and
c axis lengths of a unit cell.
eigendecomposition The collection of items making up the Eigendecomposition of a
matrix. For an n x n matrix, instances of this subcategory will
consist of n Eigenvectors of dimension n, and n Eigenvalues.
fractional_coordinate The collection of x, y, and z components of a position specified
with reference to unit cell directions.
fractional_coordinate_esd The collection of estimated standard deviations of the x, y, and
z components of a position specified with reference to unit cell
directions.
matrix The collection of elements of a matrix.
miller_index The collection of h, k, and l components of the Miller index of
a reflection.
mm_atom_site_auth_label The collection of asym id, atom id, comp id and seq id
components of an author's alternative specification for
a macromolecular atom site.
mm_atom_site_label The collection of alt id, asym id, atom id, comp id and seq id
components of the label for a macromolecular atom site.
mm_poly_res_label The collection of entity id, comp id and seq id components of the label for a residue in a polymer.
unit_vector The collection of elements of a vector whose norm equals 1.
vector The collection of elements of a vector.
Units Identifier Description
8pi2_angstroms_squared 8pi2 * angstroms squared (metres * 10(-10))2
angstroms angstroms (metres * 10(-10))
angstroms_cubed angstroms cubed (metres * 10(-10))3
angstroms_degrees angstroms * degrees
angstroms_squared angstroms squared (metres * 10(-10))2
arbitrary arbitrary system of units.
celsius degrees (of temperature) Celsius
centimetres centimetres (metres * 10( -2))
counts counts
counts_per_photon counts per photon
degrees degrees (of arc)
degrees_per_minute degrees (of arc) per minute
degrees_squared degrees squared
electron_volts electron volts
electrons electrons
electrons_angstrom_squared electrons square angstrom
electrons_per_angstroms_cubed electrons per angstroms cubed (electrons/(metres * 10(-10))(-3))
electrons_per_nanometres_cubed electrons per nanometres cubed (electrons/(metres * 10( -9))(-3))
electrons_per_picometres_cubed electrons per picometres cubed (electrons/(metres * 10(-12))(-3))
electrons_squared electrons squared
femtometres femtometres (metres * 10(-15))
femtoseconds femtoseconds (seconds * 10( -15))
gigapascals gigapascals
hertz reciprocal seconds
hours hours
ions_per_cm_squared_per_sec ions per centimetre squared per second (ions/(meters * 10(-2))(-2)/second)
joules Joules
kelvins temperature in Kelvin
kilodaltons kilodaltons
kilodaltons/nanometer kilodaltons/nanometer
kiloelectron_volts KeV (electron volts * 10( 3))
kilopascals kilopascals
kilovolts kilovolts
kilowatts kilowatts
megadaltons megadaltons
megagrams_per_cubic_metre megagrams per cubic metre
metres metres (metres)
mg_per_ml milliliter per milligram
microjoules joules * 10( -6)
microliters_per_min microliters per minute
micrometres micrometres (metres * 10( -6))
micrometres_squared micrometres squared (metres * 10( -6))2
microns micrometres (metres * 10( -6))
microns_squared micrometres squared (metres * 10( -6))2
microseconds microseconds (seconds * 10( -6))
milliamperes milliamperes
milligrams grams / 1000
milliliters liter / 1000
millimetres millimetres (metres * 10( -3))
millimolar millimolar
milliradians milliradians (of arc)
minutes minutes
ml_per_min milliliters per minute
nanometers nanometers (metres * 10( -9))
nanometres nanometres (metres * 10( -9))
nanometres_cubed nanometres cubed (metres * 10( -9))3
nanometres_squared nanometres squared (metres * 10( -9))2
nanoseconds nanoseconds (seconds * 10( -9))
pascals pascals
picometres picometres (metres * 10(-12))
picometres_cubed picometres cubed (metres * 10(-12))3
picometres_squared picometres squared (metres * 10(-12))2
pixels_per_millimetre pixels per millimetre
reciprocal_angstroms reciprocal angstroms ((metres * 10(-10))(-1))
reciprocal_centimetres reciprocal centimetres ((metres * 10( -2))(-1))
reciprocal_metres reciprocal metres (metres(-1))
reciprocal_millimetres reciprocal millimetres ((metres * 10( -3))(-1))
reciprocal_nanometres reciprocal nanometres ((metres * 10( -9))(-1))
reciprocal_picometres reciprocal picometres ((metres * 10(-12))(-1))
reciprocal_seconds reciprocal seconds (seconds(-1))
seconds seconds
teraphotons_per_pulse (photons * 10( 12)) per pulse
volts volts

Units Conversion List

From Units&Identifier To Units&Identifier Operator Conversion Factor
metres centimetres * 1.0E+02
metres millimetres * 1.0E+03
metres nanometres * 1.0E+09
metres angstroms * 1.0E+10
metres picometres * 1.0E+12
metres femtometres * 1.0E+15
centimetres millimetres * 1.0E+01
centimetres nanometres * 1.0E+07
centimetres angstroms * 1.0E+08
centimetres picometres * 1.0E+10
centimetres femtometres * 1.0E+13
millimetres centimetres * 1.0E-01
millimetres nanometres * 1.0E+06
millimetres angstroms * 1.0E+07
millimetres picometres * 1.0E+09
millimetres femtometres * 1.0E+12
nanometres centimetres * 1.0E-07
nanometres millimetres * 1.0E-06
nanometres angstroms * 1.0E+01
nanometres picometres * 1.0E+03
nanometres femtometres * 1.0E+06
angstroms centimetres * 1.0E-08
angstroms millimetres * 1.0E-07
angstroms nanometres * 1.0E-01
angstroms picometres * 1.0E+02
angstroms femtometres * 1.0E+05
picometres centimetres * 1.0E-10
picometres millimetres * 1.0E-09
picometres nanometres * 1.0E-03
picometres angstroms * 1.0E-02
picometres femtometres * 1.0E+03
femtometres centimetres * 1.0E-13
femtometres millimetres * 1.0E-12
femtometres nanometres * 1.0E-06
femtometres angstroms * 1.0E-05
femtometres picometres * 1.0E-03
reciprocal_centimetres reciprocal_millimetres * 1.0E-01
reciprocal_centimetres reciprocal_nanometres * 1.0E-07
reciprocal_centimetres reciprocal_angstroms * 1.0E-08
reciprocal_centimetres reciprocal_picometres * 1.0E-10
reciprocal_millimetres reciprocal_centimetres * 1.0E+01
reciprocal_millimetres reciprocal_nanometres * 1.0E-06
reciprocal_millimetres reciprocal_angstroms * 1.0E-07
reciprocal_millimetres reciprocal_picometres * 1.0E-09
reciprocal_nanometres reciprocal_centimetres * 1.0E+07
reciprocal_nanometres reciprocal_millimetres * 1.0E+06
reciprocal_nanometres reciprocal_angstroms * 1.0E-01
reciprocal_nanometres reciprocal_picometres * 1.0E-03
reciprocal_angstroms reciprocal_centimetres * 1.0E+08
reciprocal_angstroms reciprocal_millimetres * 1.0E+07
reciprocal_angstroms reciprocal_nanometres * 1.0E+01
reciprocal_angstroms reciprocal_picometres * 1.0E-02
reciprocal_picometres reciprocal_centimetres * 1.0E+10
reciprocal_picometres reciprocal_millimetres * 1.0E+09
reciprocal_picometres reciprocal_nanometres * 1.0E+03
reciprocal_picometres reciprocal_angstroms * 1.0E+01
nanometres_squared angstroms_squared * 1.0E+02
nanometres_squared picometres_squared * 1.0E+06
angstroms_squared nanometres_squared * 1.0E-02
angstroms_squared picometres_squared * 1.0E+04
angstroms_squared 8pi2_angstroms_squared * 78.9568
picometres_squared nanometres_squared * 1.0E-06
picometres_squared angstroms_squared * 1.0E-04
nanometres_cubed angstroms_cubed * 1.0E+03
nanometres_cubed picometres_cubed * 1.0E+09
angstroms_cubed nanometres_cubed * 1.0E-03
angstroms_cubed picometres_cubed * 1.0E+06
picometres_cubed nanometres_cubed * 1.0E-09
picometres_cubed angstroms_cubed * 1.0E-06
kilopascals gigapascals * 1.0E-06
gigapascals kilopascals * 1.0E+06
hours minutes * 6.0E+01
hours seconds * 3.6E+03
hours microseconds * 3.6E+09
minutes hours / 6.0E+01
minutes seconds * 6.0E+01
minutes microseconds * 6.0E+07
seconds hours / 3.6E+03
seconds minutes / 6.0E+01
seconds microseconds * 1.0E+06
microseconds hours / 3.6E+09
microseconds minutes / 6.0E+07
microseconds seconds / 1.0E+06
celsius kelvins - 273.0
kelvins celsius + 273.0
electrons_per_nanometres_cubed electrons_per_angstroms_cubed * 1.0E+03
electrons_per_nanometres_cubed electrons_per_picometres_cubed * 1.0E+09
electrons_per_angstroms_cubed electrons_per_nanometres_cubed * 1.0E-03
electrons_per_angstroms_cubed electrons_per_picometres_cubed * 1.0E+06
electrons_per_picometres_cubed electrons_per_nanometres_cubed * 1.0E-09
electrons_per_picometres_cubed electrons_per_angstroms_cubed * 1.0E-06