Dictionary Index ihm-extension.dic
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General 
- Dictionary title
- Integrative/Hybrid (I/H) methods extension dictionary
- Dictionary description
- The I/H methods dictionary is an extension of the PDBx/mmCIF dictionary. This dictionary is actively developed and maintained in a github repository available at https://github.com/ihmwg/IHM-dictionary. I/H structural models that are compliant to this extension dictionary can be deposited to the PDB-Dev prototype deposition and archiving system (https://pdb-dev.wwpdb.org).
- Original developers
- wwPDB I/H methods task force members
- Dictionary maintainers
- wwPDB I/H methods task force members
- Dictionary name
- ihm-extension.dic
- Dictionary version
- 1.12
- Last update
- 2020-07-10
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Dictionary Revision History
| Version | Revision Date | Revision Description | |
|---|---|---|---|
| 1.12 | 2020-07-10 | Changes (bv): + Added enumerations to _ihm_cross_link_list.linker_type |
ihm-extension.dic |
| 1.11 | 2020-07-03 | Changes (bv): + Added ihm_hdx_restraint |
ihm-extension.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 |
ihm-extension.dic |
| 1.09 | 2020-03-19 | Changes (bv): + Added ihm_data_transformation + Added _ihm_related_datasets.transformation_id |
ihm-extension.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 |
ihm-extension.dic |
| 1.07 | 2020-02-10 | Changes (bv): + Added CYS to _ihm_cross_link_list.linker_type enumeration list |
ihm-extension.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 |
ihm-extension.dic |
| 1.05 | 2019-11-15 | Changes (bv): + Added BMSO and DHSO to _ihm_cross_link_list.linker_type enumeration list |
ihm-extension.dic |
| 1.04 | 2019-10-10 | Changes (bv): + Added _ihm_derived_distance_restraint.mic_value + Added enumeration to _ihm_dataset_list.data_type |
ihm-extension.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 |
ihm-extension.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 |
ihm-extension.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. |
ihm-extension.dic |
| 1.0 | 2019-05-31 | Changes (bv): + Updated several categories to fix primary key information and parent-child relationships |
ihm-extension.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 |
ihm-extension.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 |
ihm-extension.dic |
| 0.139 | 2019-01-03 | Changes (bv): + Changed IHM_FEATURE_PSEUDO_SITE to IHM_PSEUDO_SITE_FEATURE |
ihm-extension.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 |
ihm-extension.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 |
ihm-extension.dic |
| 0.136 | 2018-10-05 | Changes (bv): + Added ihm_hydroxyl_radical_fp_restraint |
ihm-extension.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 |
ihm-extension.dic |
| 0.134 | 2018-07-18 | Changes (bv): + Updated _item_sub_category.id for matrices and vectors |
ihm-extension.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 |
ihm-extension.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 |
ihm-extension.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 |
ihm-extension.dic |
| 0.130 | 2018-04-19 | Changes (bv): + Updated enumeration for ihm_dataset_related_db_reference.db_name and ihm_dataset_list.data_type |
ihm-extension.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 |
ihm-extension.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 |
ihm-extension.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 |
ihm-extension.dic |
| 0.126 | 2018-02-06 | Changes (bv): + Updated enumeration list for _ihm_dataset_list.data_type |
ihm-extension.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 |
ihm-extension.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 |
ihm-extension.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 |
ihm-extension.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 |
ihm-extension.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 |
ihm-extension.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 |
ihm-extension.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 |
ihm-extension.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 |
ihm-extension.dic |
| 0.117 | 2017-11-09 | Changes (bv): + Updated description for _ihm_starting_model_details.starting_model_sequence_offset |
ihm-extension.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 |
ihm-extension.dic |
| 0.115 | 2017-10-12 | Changes (bv): + Added _ihm_modeling_post_process.feature_name + Fixed enumeration for _ihm_cross_link_list.linker_type |
ihm-extension.dic |
| 0.114 | 2017-10-09 | Changes (bv): + Fixed typos and syntax |
ihm-extension.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 |
ihm-extension.dic |
| 0.112 | 2017-10-04 | Changes (bv): + Added _ihm_dataset_list.details + Added enumeration to _ihm_dataset_list.data_type |
ihm-extension.dic |
| 0.111 | 2017-10-04 | Changes (bv): + Removed _ihm_cross_link_restraint.linker_type + Updated enumerations to _ihm_cross_link_restraint.restraint_type |
ihm-extension.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 |
ihm-extension.dic |
| 0.109 | 2017-09-28 | Changes (bv): + Added _ihm_model_list.representation_id + Added _atom_site.ihm_model_id |
ihm-extension.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 |
ihm-extension.dic |
| 0.107 | 2017-07-17 | Changes (ep/bv): + Added category_group_list, item_type_list and item_units_list categories |
ihm-extension.dic |
| 0.106 | 2017-07-13 | Changes (bv): + Updated dictionary description and version history |
ihm-extension.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 |
ihm-extension.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 |
ihm-extension.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 |
ihm-extension.dic |
| 0.102 | 2017-03-29 | Changes (bv): + Updated examples in IHM_STARTING_COMPARATIVE_MODELS |
ihm-extension.dic |
| 0.101 | 2017-03-29 | Changes (bv): + Updated _ihm_starting_model_seq_dif.db_entity_id as non-mandatory |
ihm-extension.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 |
ihm-extension.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 |
ihm-extension.dic |