Dictionary Index ihm-extension.dic

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
0.137
Last update
2018-10-26

Dictionary Revision History

Version Revision Date Revision Description
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
0.136 2018-10-5
Changes (bv):
+ Added ihm_hydroxyl_radical_fp_restraint
0.135 2018-10-4
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
0.134 2018-07-18
Changes (bv):
+ Updated _item_sub_category.id for matrices and vectors
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
0.132 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
0.131 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
0.130 2018-04-19
Changes (bv):
+ Updated enumeration for ihm_dataset_related_db_reference.db_name and ihm_dataset_list.data_type
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
0.128 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
0.127 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
0.126 2018-02-06
Changes (bv):
+ Updated enumeration list for _ihm_dataset_list.data_type
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
0.124 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
0.123 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
0.122 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
0.121 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
0.120 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
0.119 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
0.118 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
0.117 2017-11-09
Changes (bv):
+ Updated description for _ihm_starting_model_details.starting_model_sequence_offset
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
0.115 2017-10-12
Changes (bv):
+ Added _ihm_modeling_post_process.feature_name
+ Fixed enumeration for _ihm_cross_link_list.linker_type
0.114 2017-10-09
Changes (bv):
+ Fixed typos and syntax
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
0.112 2017-10-04
Changes (bv):
+ Added _ihm_dataset_list.details
+ 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
0.110 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
0.109 2017-09-28
Changes (bv):
+ Added _ihm_model_list.representation_id
+ Added _atom_site.ihm_model_id
0.108 2017-09-12
Changes (bv):
+ Added IHM_STRUCT_ASSEMBLY_CLASS, IHM_STRUCT_ASSEMBLY_CLASS_LIST
+ Added _ihm_struct_assembly.parent_assembly_id
0.107 2017-07-17
Changes (ep/bv):
+ Added category_group_list, item_type_list and item_units_list categories
0.106 2017-07-13
Changes (bv):
+ Updated dictionary description and version history
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
0.104 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
0.103 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
0.102 2017-03-29
Changes (bv):
+ Updated examples in IHM_STARTING_COMPARATIVE_MODELS
0.101 2017-03-29
Changes (bv):
+ Updated _ihm_starting_model_seq_dif.db_entity_id as non-mandatory
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
0.000 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