data_mmcif_ihm_ext.dic _datablock.id mmcif_ihm_ext.dic _datablock.description ; This data block holds the extension dictionary for Integrative/Hybrid (I/H) methods. This extension is based on the PDBx/mmCIF dictionary. This resource is actively developed and maintained in a github repository available at https://github.com/ihmwg/IHMCIF. I/H structural models that are compliant to this extension dictionary can be deposited to the PDB-Dev prototype deposition and archiving system (https://pdb-dev.wwpdb.org). ; # _dictionary.title mmcif_ihm_ext.dic _dictionary.datablock_id mmcif_ihm_ext.dic _dictionary.version 1.25 # loop_ _dictionary_history.version _dictionary_history.update _dictionary_history.revision 0.000 2017-03-20 ; Changes (jdw/bv) + Release as initial version 0.000 + Changed _imp to _ihm + Changed _imp_template_details to _ihm_starting_model_details + Changed _imp_tempate_model_coord to _ihm_starting_model_coord + Changed _imp_pseudo_atom_site to _ihm_sphere_object_site + Added enumeration 'integrative' to _ihm_starting_model_details.starting_model_source + Separated ihm_cross_link_restraint and ihm_cross_link_list categories + Updated ambiguous crosslinks in ihm_cross_link_restraint and ihm_cross_link_list categories + Added ihm_dataset_list, ihm_related_database_reference and ihm_dataset_other categories + Added ihm_cross_link_result (yet to be completed) and ihm_entity_assembly categories + Updated ihm_2dem_class_average_restraint category + Removed ihm_cross_link_db_reference, ihm_cross_link_reference_auxiliary, ihm_2dem_class_average categories + Revised several data items to be non-mandatory + Changed category key item in ihm_model_details category to account for multiple coarse-grained representations of the same model segment (introduced _ihm_model_details.ordinal_id) + Updated _ihm_sphere_obj_site.entity_instance_id, ihm_cross_link_restraint (psi and sigma parameters) + Added ihm_modeling_protocol, ihm_cluster_info, ihm_struct_assembly (previously ihm_entity_assembly) + Added _ihm_3dem_restraint category; minor changes to other categories + Changed ihm_model_details category name to ihm_model_representation (handles multi-scale representation) + Changed several data items in the ihm_modeling_protocol category + Added ihm_modeling_post_process, ihm_model_list, ihm_multi_state_modeling, ihm_time_ordered_ensemble, ihm_gaussian_object_site categories + Linked ihm_model_list to ihm_sphere_obj_site through model_id + Linked ihm_starting_model_details to ihm_dataset_list through dataset_list_id + Added new data item _ihm_model_representation.representation_id and more changes to ihm_modeling_protocol and ihm_gaussian_obj_site categories. + Added ihm_gaussian_obj_ensemble category to represent ensembles as gaussian objects - to be different from + ihm_gaussian_object_site category that is used in model representation and hence by visualization software. + Changed ihm_cluster_info category name to ihm_ensemble_info and changed relevant data item names accordingly. + Changed ihm_related_database_reference category name to ihm_dataset_related_db_reference to be consistent with other similar categories + Minor changes in other categories: ihm_model_list, ihm_dataset_list, ihm_modeling_protocol, ihm_ensemble_info, ihm_multi_state_modeling, ihm_time_ordered_ensemble, ihm_2dem_class_average_restraint (data items are now similar to 2D class average images in EMPIAR), ihm_model_represenation. + Updated parent-child relationships across several categories (ihm_modeling_protocol, ihm_ensemble_info ihm_model_list, ihm_multi_state_modeling, ihm_time_ordered_ensemble, ihm_2dem_class_average_fitting, ihm_cross_link_result) + Updated examples in ihm_dataset_list, ihm_dataset_other and ihm_dataset_related_db_reference + Changed ihm_modeling_experiment to ihm_modeling_protocol to be consistent with the model archive naming convention + Added ihm_sas_restraint category; added _ihm_3dem_restraint.map_segment_flag + Modified the following categories: ihm_model_list, ihm_modeling_protocol, ihm_multi_state_modeling, ihm_time_ordered_ensemble + Minor updates to ihm_cross_link_list, ihm_cross_link_restraint and ihm_model_representation categories. + Added _ihm_sphere_obj_site.rmsf and _ihm_starting_model_details.asym_id + Added ihm_related_datasets and ihm_cross_link_result_parameters + Added _ihm_3dem_restraint.struct_assembly_id, _ihm_sas_restraint.struct_assembly_id, _ihm_starting_model_details.notes and _ihm_starting_model_coord.group_PDB + Changed _ihm_3dem_restraint.id to _ihm_3dem_restraint.ordinal_id and _ihm_sas_restraint.id to _ihm_sas_restraint.ordinal_id + Changed _ihm_dataset_related_db_reference.access_code to _ihm_dataset_related_db_reference.accession_code + Added new categories to reference externally hosted files: IHM_LOCALIZATION_DENSITY_FILES, + IHM_STARTING_MODEL_ALIGNMENT_FILES, IHM_MODELING_WORKFLOW_FILES + Added IHM_DATA_DOI_URL_INFO category to include a URL corresponding to a DOI. This enables automated download of files. + Removed redundant DOI references from several categories + Added _ihm_starting_model_details.starting_model_sequence_offset + Changed _ihm_starting_model_details.starting_model_db_pdb_auth_asym_id to _ihm_starting_model_details.starting_model_auth_asym_id + Changed IHM_DOI_URL_INFO to IHM_EXTERNAL_REFERENCE_INFO; modified all downstream dependencies + Changed IHM_DATASET_OTHER to IHM_DATASET_EXTERNAL_REFERENCE_DETAILS; modified all downstream dependencies + Modified definitions within IHM_EXTERNAL_REFERENCE_INFO + Added IHM_EXTERNAL_FILES category; Removed IHM_STARTING_MODEL_ALIGNMENT_FILES category + Changed IHM_MODELING_WORKFLOW_FILES, IHM_LOCALIZATION_DENSITY_FILES + Changed IHM_DATASET_EXTERNAL_REFERENCE_DETAILS to IHM_DATASET_EXTERNAL_REFERENCE + Modified IHM_STARTING_MODEL_DETAILS category + Added IHM_STARTING_COMPARATIVE_MODELS category + Added IHM_STARTING_MODEL_SEQ_DIF category; removed _ihm_starting_model_details.notes + Updated IHM_ENSEMBLE_INFO, IHM_EXTERNAL_FILES and IHM_EXTERNAL_REFERENCE_INFO + Added _ihm_multi_state_modeling.experiment_type; updated IHM_ENSEMBLE_INFO ; 0.100 2017-03-23 ; Changes (bv): + Release as provisional version 0.100 + Added _ihm_external_files.content_type + Added _ihm_external_files.details + Removed IHM_MODELING_WORKFLOW_FILES ; 0.101 2017-03-29 ; Changes (bv): + Updated _ihm_starting_model_seq_dif.db_entity_id as non-mandatory ; 0.102 2017-03-29 ; Changes (bv): + Updated examples in IHM_STARTING_COMPARATIVE_MODELS ; 0.103 2017-03-30 ; Changes (bv): + Updated IHM_STARTING_MODEL_DETAILS + Updated IHM_STARTING_COMPARATIVE_MODELS + Updated IHM_DATASET_LIST, IHM_RELATED_DATASETS + Updated IHM_DATASET_RELATED_DB_REFERENCE + Updated IHM_DATASET_EXTERNAL_REFERENCE + Added examples to IHM_EXTERNAL_REFERENCE_INFO and IHM_EXTERNAL_FILES ; 0.104 2017-04-19 ; Changes (bv): + Updated IHM_STARTING_MODEL_DETAILS + Updated IHM_STARTING_COMPARATIVE_MODELS + Updated IHM_STARTING_MODEL_SEQ_DIF + Updated IHM_MODEL_REPRESENTATION + Updated IHM_DATASET_LIST + Added IHM_DATASET_GROUP + Updated IHM_MODELING_PROTOCOL ; 0.105 2017-05-25 ; Changes (bv): + Added item description to _ihm_ensemble_info.ensemble_file_id + Added item description to _ihm_2dem_class_average_restraint.pixel_size_width + Added item description to _ihm_2dem_class_average_restraint.pixel_size_height + Added category description to ihm_2dem_class_average_fitting + Added enumeration 'DCD' to _ihm_external_files.file_format + Changed _ihm_external_files.file_size_kb to _ihm_external_files.file_size_bytes ; 0.106 2017-07-13 ; Changes (bv): + Updated dictionary description and version history ; 0.107 2017-07-17 ; Changes (ep/bv): + Added category_group_list, item_type_list and item_units_list categories ; 0.108 2017-09-12 ; Changes (bv): + Added IHM_STRUCT_ASSEMBLY_CLASS, IHM_STRUCT_ASSEMBLY_CLASS_LIST + Added _ihm_struct_assembly.parent_assembly_id ; 0.109 2017-09-28 ; Changes (bv): + Added _ihm_model_list.representation_id + Added _atom_site.ihm_model_id ; 0.110 2017-10-03 ; Changes (bv): + Added _ihm_cross_link_restraint.atom_id_1, _ihm_cross_link_restraint.atom_id_2 + Added _ihm_cross_link_restraint.restraint_type + Changed _ihm_cross_link_restraint.type to _ihm_cross_link_restraint.linker_type + Changed _ihm_cross_link_list.type to _ihm_cross_link_list.linker_type + Added enumerations to _ihm_cross_link_restraint.linker_type and _ihm_cross_link_list.linker_type + Added enumeration to and changed _item.mandatory_code of _ihm_cross_link_restraint.model_granularity + Added ihm_predicted_contact_restraint category + Added enumeration to _ihm_dataset_list.data_type ; 0.111 2017-10-04 ; Changes (bv): + Removed _ihm_cross_link_restraint.linker_type + Updated enumerations to _ihm_cross_link_restraint.restraint_type ; 0.112 2017-10-04 ; Changes (bv): + Added _ihm_dataset_list.details + Added enumeration to _ihm_dataset_list.data_type ; 0.113 2017-10-06 ; Changes (bv): + Added IHM_MODEL_REPRESENTATIVE + Added enumeration to _ihm_cross_link_list.linker_type + Updated item description for _ihm_predicted_contact_restraint.probability ; 0.114 2017-10-09 ; Changes (bv): + Fixed typos and syntax ; 0.115 2017-10-12 ; Changes (bv): + Added _ihm_modeling_post_process.feature_name + Fixed enumeration for _ihm_cross_link_list.linker_type ; 0.116 2017-10-16 ; Changes (bv): + Updated _item_description.description for _ihm_model_list.model_group_id + Updated enumerations for _ihm_dataset_list.data_type + Updated parent-child relationships within _ihm_model_list.model_id ; 0.117 2017-11-09 ; Changes (bv): + Updated description for _ihm_starting_model_details.starting_model_sequence_offset ; 0.118 2017-12-06 ; Changes (bv): + Changed ihm_time_ordered_ensemble to ihm_ordered_ensemble with appropriate revisions to the category + Changed _ihm_modeling_protocol.time_ordered_flag to _ihm_modeling_protocol.ordered_flag + Changed mandatory code for _ihm_model_list.representation_id + Added an example to ihm_model_list category ; 0.119 2017-12-07 ; Changes (bv): + Changed ihm_ordered_ensemble.ordered_process_id to ihm_ordered_ensemble.process_id + Changed ihm_ordered_ensemble.ordered_process_description to ihm_ordered_ensemble.process_description. + Changed parent-child relationships for _ihm_predicted_contact_restraint.atom_id_1, _ihm_predicted_contact_restraint.atom_id_2, _ihm_cross_link_restraint.atom_id_1, _ihm_cross_link_restraint.atom_id_2, _ihm_starting_model_coord.atom_id ; 0.120 2018-01-10 ; Changes (bv): + Added ihm_feature_selection_atom, ihm_feature_selection_residue, ihm_derived_distance_restraint + Fixed typos in the parent name of _ihm_predicted_contact_restraint.atom_id_1 and _ihm_predicted_contact_restraint.atom_id_2 + Fixed _item_type.code in _ihm_starting_model_coord.atom_id ; 0.121 2018-01-17 ; Changes (bv): + Added _ihm_derived_distance_restraint.distance_upper_limit_std and _ihm_derived_distance_restraint.distance_lower_limit_std + Updated _item_type.code for _ihm_external_reference_info.reference_type and _ihm_external_reference_info.reference_provider ; 0.122 2018-01-22 ; Changes (bv): + Updated parent-child relationships for _ihm_model_representation.entity_id, _ihm_struct_assembly.entity_id, _ihm_feature_selection_atom.entity_id, _ihm_feature_selection_residue.entity_id + Changed _ihm_derived_distance_restraint.distance_lower_limit_std to _ihm_derived_distance_restraint.distance_lower_limit_esd + Changed _ihm_derived_distance_restraint.distance_upper_limit_std to _ihm_derived_distance_restraint.distance_upper_limit_esd + Added enumeration for _ihm_external_reference_info.refers_to and _ihm_external_files.file_format ; 0.123 2018-01-24 ; Changes (bv): + Added IHM_STRUCT_ASSEMBLY_DETAILS category. + Updated parent-child relationships for _ihm_starting_model_details.entity_description, _ihm_model_representation.entity_description, _ihm_struct_assembly.entity_description, _ihm_predicted_contact_restraint.entity_description_1, _ihm_cross_link_list.entity_description_1, _ihm_predicted_contact_restraint.entity_description_2, _ihm_cross_link_list.entity_description_2 ; 0.124 2018-02-01 ; Changes (bv): + Updated parent-child relationships for _ihm_model_representation.entity_id, _ihm_struct_assembly.entity_id + Added IHM_FEATURE_LIST and IHM_NON_POLY_ATOM_FEATURE categories. + Changed IHM_FEATUTE_SELECTION_ATOM to IHM_POLY_ATOM_FEATURE. + Changed IHM_FEATUTE_SELECTION_RESDIUE to IHM_POLY_RESIDUE_FEATURE. + Updated IHM_DERIVED_DISTANCE_RESTRAINT ; 0.125 2018-02-05 ; Changes (bv): + Added _ihm_derived_distance_restraint.random_exclusion_fraction + Changed _ihm_derived_distance_restraint.conditionality to _ihm_derived_distance_restraint.group_conditionality + Updated description for _ihm_derived_distance_restraint.group_conditionality ; 0.126 2018-02-06 ; Changes (bv): + Updated enumeration list for _ihm_dataset_list.data_type ; 0.127 2018-02-26 ; Changes (bv): + Added _ihm_poly_residue_feature.residue_range_granularity, _ihm_poly_residue_feature.rep_atom + Updated enumeration for _ihm_cross_link_list.linker_type, _ihm_external_files.content_type ; 0.128 2018-03-16 ; Changes (bv): + Added _ihm_dataset_group.application and _ihm_dataset_group.details + Updated enumeration for _ihm_modeling_post_process.type + Fixed typos ; 0.129 2018-03-22 ; Changes (bv): + Added _ihm_modeling_post_process.struct_assembly_id and _ihm_modeling_post_process.dataset_group_id + Added ihm_residues_not_modeled ; 0.130 2018-04-19 ; Changes (bv): + Updated enumeration for ihm_dataset_related_db_reference.db_name and ihm_dataset_list.data_type ; 0.131 2018-05-21 ; Changes (bv): + Added _ihm_modeling_post_process.software_id, _ihm_modeling_protocol.software_id + Added _ihm_multi_state_modeling.population_fraction_sd + Added _ihm_starting_comparative_models.software_id, _ihm_starting_comparative_models.script_file_id + Updated enumeration for _ihm_starting_model_details.starting_model_source + Updated _item.mandatory_code for _ihm_starting_comparative_models.starting_model_seq_id_begin + Updated _item.mandatory_code for _ihm_starting_comparative_models.starting_model_seq_id_end ; 0.132 2018-05-25 ; Changes (bv): + Added IHM_STARTING_COMPUTATIONAL_MODELS + Removed _ihm_starting_comparative_models.software_id, _ihm_starting_comparative_models.script_file_id + Added _ihm_modeling_post_process.script_file_id, _ihm_modeling_protocol.script_file_id ; 0.133 2018-06-29 ; Changes (bv): + Added IHM_GEOMETRIC_OBJECT_LIST, IHM_GEOMETRIC_OBJECT_CENTER, IHM_GEOMETRIC_OBJECT_TRANSFORMATION + Added IHM_GEOMETRIC_OBJECT_SPHERE, IHM_GEOMETRIC_OBJECT_TORUS, IHM_GEOMETRIC_OBJECT_HALF_TORUS + Added IHM_GEOMETRIC_OBJECT_AXIS, IHM_GEOMETRIC_OBJECT_PLANE, IHM_GEOMETRIC_OBJECT_DISTANCE_RESTRAINT ; 0.134 2018-07-18 ; Changes (bv): + Updated _item_sub_category.id for matrices and vectors ; 0.135 2018-10-04 ; Changes (bv): + Added DSSO crosslinker + Updated parent-child relationships for several data items: _ihm_starting_model_details.entity_id, _ihm_model_representation.entity_id, _ihm_struct_assembly.entity_id, _ihm_localization_density_files.entity_id, _ihm_starting_model_coord.entity_id, _ihm_starting_model_coord.comp_id, _ihm_sphere_obj_site.entity_id, _ihm_gaussian_obj_site.entity_id, _ihm_gaussian_obj_ensemble.entity_id + Updated _item_type.code for _ihm_external_files.file_path ; 0.136 2018-10-05 ; Changes (bv): + Added ihm_hydroxyl_radical_fp_restraint ; 0.137 2018-10-26 ; Changes (bv): + Renamed IHM_NON_POLY_ATOM_FEATURE to IHM_NON_POLY_FEATURE + Updated _ihm_feature_list.feature_type + Added IHM_FEATURE_PSEUDO_SITE ; 0.138 2018-12-20 ; Changes (bv): + Added _ihm_modeling_protocol.ensemble_flag + Changed _item.type_code from code to ucode for: _ihm_modeling_protocol.multi_scale_flag _ihm_modeling_protocol.multi_state_flag _ihm_modeling_protocol.ordered_flag _ihm_dataset_list.database_hosted _ihm_2dem_class_average_restraint.image_segment_flag _ihm_3dem_restraint.map_segment_flag _ihm_sas_restraint.profile_segment_flag + Updated definitions for _ihm_feature_list.entity_type + Updated enumeration list for _ihm_feature_list.feature_type ; 0.139 2019-01-03 ; Changes (bv): + Changed IHM_FEATURE_PSEUDO_SITE to IHM_PSEUDO_SITE_FEATURE ; 0.140 2019-03-11 ; Changes (bv): + Added IHM_INTERFACE_RESIDUE_FEATURE + Added _ihm_poly_residue_feature.interface_residue_flag + Updated item_mandatory.code for _ihm_poly_residue_feature.asym_id _ihm_poly_atom_feature.asym_id, _ihm_non_poly_feature.asym_id ; 0.141 2019-05-06 ; Changes (bv): + Added IHM_CHEMICAL_COMPONENT_DESCRIPTOR, IHM_PROBE_LIST, IHM_EPR_RESTRAINT + Added IHM_POLY_PROBE_POSITION, IHM_POLY_PROBE_CONJUGATE + Added IHM_LIGAND_PROBE + Added _ihm_cross_link_list.linker_chem_comp_descriptor_id ; 1.0 2019-05-31 ; Changes (bv): + Updated several categories to fix primary key information and parent-child relationships ; 1.01 2019-07-26 ; Changes (bv): + Updated _item_mandatory.code and _pdbx_item.mandatory_code for several data items. + Added _item_sub_category.id in ihm_poly_probe_position. + Added PDB-Dev to the enumeration list in ihm_dataset_related_db_reference.db_name. ; 1.02 2019-10-01 ; Changes (bv): + Added _ihm_starting_model_details.description, _ihm_starting_comparative_models.details + Added _ihm_model_representation_details.description, _ihm_modeling_protocol_details.description + Added _ihm_modeling_post_process.details, _ihm_ensemble_info.details + Added _ihm_external_reference_info.details, _ihm_cross_link_list.details + Added _ihm_feature_list.details, _ihm_geometric_object_half_torus.details + Added enumerations (DSG and BSP) to _ihm_cross_link_list.linker_type + Updated _item_enumeration.detail for items in _ihm_cross_link_list.linker_type + Updated _item_description.description for _ihm_external_files.details ; 1.03 2019-10-03 ; Changes (bv): + Changed _ihm_geometric_object_distance_restraint.other_details to _ihm_geometric_object_distance_restraint.details + Removed _ihm_geometric_object_list.other_details and _ihm_geometric_object_half_torus.details ; 1.04 2019-10-10 ; Changes (bv): + Added _ihm_derived_distance_restraint.mic_value + Added enumeration to _ihm_dataset_list.data_type ; 1.05 2019-11-15 ; Changes (bv): + Added BMSO and DHSO to _ihm_cross_link_list.linker_type enumeration list ; 1.06 2020-01-24 ; Changes (bv): + Added _ihm_cross_link_restraint.pseudo_site_flag + Added ihm_cross_link_pseudo_site category + Added ihm_pseudo_site category + Removed _ihm_pseudo_site_feature.Cartn_x, _ihm_pseudo_site_feature.Cartn_y _ihm_pseudo_site_feature.Cartn_z, _ihm_pseudo_site_feature.radius _ihm_pseudo_site_feature.description + Added _ihm_pseudo_site_feature.pseudo_site_id ; 1.07 2020-02-10 ; Changes (bv): + Added CYS to _ihm_cross_link_list.linker_type enumeration list ; 1.08 2020-02-14 ; Changes (bv): + Added _ihm_ensemble_info.sub_sample_flag, _ihm_ensemble_info.sub_sampling_type + Added ihm_ensemble_sub_sample ; 1.09 2020-03-19 ; Changes (bv): + Added ihm_data_transformation + Added _ihm_related_datasets.transformation_id ; 1.10 2020-06-04 ; Changes (bv): + Added ihm_derived_angle_restraint, ihm_derived_dihedral_restraint + Added _ihm_derived_distance_restraint.distance_threshold_mean + Added _ihm_derived_distance_restraint.distance_threshold_esd + Updated enumeration for _ihm_derived_distance_restraint.restraint_type + Updated enumeration for _ihm_dataset_list.data_type ; 1.11 2020-07-03 ; Changes (bv): + Added ihm_hdx_restraint ; 1.12 2020-07-10 ; Changes (bv): + Added enumerations to _ihm_cross_link_list.linker_type ; 1.13 2021-01-28 ; Changes (bv): + Added enumerations to _ihm_cross_link_list.linker_type ; 1.14 2021-03-04 ; Changes (bv): + Added enumerations to _ihm_cross_link_list.linker_type ; 1.15 2021-03-16 ; Changes (bv): + Added enumerations to _ihm_dataset_related_db_reference.db_name ; 1.16 2021-04-14 ; Changes (bv): + Added enumerations to _ihm_cross_link_list.linker_type ; 1.17 2021-05-21 ; Changes (bv): + Added enumerations to _ihm_cross_link_list.linker_type ; 1.18 2022-12-20 ; Changes (bv): + Added _ihm_ensemble_info.model_group_superimposed_flag + Added enumerations to _ihm_dataset_list.data_type and _ihm_ensemble_info.ensemble_clustering_method + Added ihm_entry_collection and ihm_entry_collection_mapping ; 1.19 2023-02-02 ; Changes (bv): + Added enumerations to _ihm_cross_link_list.linker_type and _ihm_dataset_related_db_reference.db_name ; 1.20 2023-02-19 ; Changes (bv): + Updated category keys for ihm_entry_collection_mapping + Added enumerations to _ihm_cross_link_list.linker_type and _ihm_dataset_related_db_reference.db_name + Add nanoseconds to item_units_list ; 1.21 2023-03-24 ; Changes (bv): + Added enumerations to _ihm_cross_link_list.linker_type ; 1.22 2023-05-26 ; Changes (bv): + Added enumerations to _ihm_dataset_related_db_reference.db_name ; 1.23 2023-07-05 ; Changes (bv): + Added enumerations to _ihm_cross_link_list.linker_type ; 1.24 2023-11-30 ; Changes (bv): + Added ihm_multi_state_scheme, ihm_multi_state_scheme_connectivity + Added ihm_kinetic_rate, ihm_relaxation_time, ihm_relaxation_time_multi_state_scheme ; 1.25 2023-12-22 ; + Rename dictionary + Reorganize repository ; # loop_ _pdbx_dictionary_component.datablock_id _pdbx_dictionary_component.dictionary_component_id _pdbx_dictionary_component.title _pdbx_dictionary_component.version mmcif_ihm-data.dic mmcif_ihm-data.dic "IHMCIF dictionary: mmcif_ihm-data" 1.0 entity_poly_seq.dic entity_poly_seq.dic "entity_poly_seq for IHMCIF" 0.001 mmcif_ihm-core.dic mmcif_ihm-core.dic "IHMCIF dictionary: mmcif_ihm-core" 1.25 # loop_ _pdbx_dictionary_component_history.dictionary_component_id _pdbx_dictionary_component_history.version _pdbx_dictionary_component_history.update _pdbx_dictionary_component_history.revision mmcif_ihm-data.dic 1.0 2023-12-22 ; Changes (bv) + Updated dictionary files organization ; entity_poly_seq.dic 0.001 2023-12-22 ; Changes (bv) + Release as initial version 0.001 ; mmcif_ihm-core.dic 0.000 2017-03-20 ; Changes (jdw/bv) + Release as initial version 0.000 + Changed _imp to _ihm + Changed _imp_template_details to _ihm_starting_model_details + Changed _imp_tempate_model_coord to _ihm_starting_model_coord + Changed _imp_pseudo_atom_site to _ihm_sphere_object_site + Added enumeration 'integrative' to _ihm_starting_model_details.starting_model_source + Separated ihm_cross_link_restraint and ihm_cross_link_list categories + Updated ambiguous crosslinks in ihm_cross_link_restraint and ihm_cross_link_list categories + Added ihm_dataset_list, ihm_related_database_reference and ihm_dataset_other categories + Added ihm_cross_link_result (yet to be completed) and ihm_entity_assembly categories + Updated ihm_2dem_class_average_restraint category + Removed ihm_cross_link_db_reference, ihm_cross_link_reference_auxiliary, ihm_2dem_class_average categories + Revised several data items to be non-mandatory + Changed category key item in ihm_model_details category to account for multiple coarse-grained representations of the same model segment (introduced _ihm_model_details.ordinal_id) + Updated _ihm_sphere_obj_site.entity_instance_id, ihm_cross_link_restraint (psi and sigma parameters) + Added ihm_modeling_protocol, ihm_cluster_info, ihm_struct_assembly (previously ihm_entity_assembly) + Added _ihm_3dem_restraint category; minor changes to other categories + Changed ihm_model_details category name to ihm_model_representation (handles multi-scale representation) + Changed several data items in the ihm_modeling_protocol category + Added ihm_modeling_post_process, ihm_model_list, ihm_multi_state_modeling, ihm_time_ordered_ensemble, ihm_gaussian_object_site categories + Linked ihm_model_list to ihm_sphere_obj_site through model_id + Linked ihm_starting_model_details to ihm_dataset_list through dataset_list_id + Added new data item _ihm_model_representation.representation_id and more changes to ihm_modeling_protocol and ihm_gaussian_obj_site categories. + Added ihm_gaussian_obj_ensemble category to represent ensembles as gaussian objects - to be different from + ihm_gaussian_object_site category that is used in model representation and hence by visualization software. + Changed ihm_cluster_info category name to ihm_ensemble_info and changed relevant data item names accordingly. + Changed ihm_related_database_reference category name to ihm_dataset_related_db_reference to be consistent with other similar categories + Minor changes in other categories: ihm_model_list, ihm_dataset_list, ihm_modeling_protocol, ihm_ensemble_info, ihm_multi_state_modeling, ihm_time_ordered_ensemble, ihm_2dem_class_average_restraint (data items are now similar to 2D class average images in EMPIAR), ihm_model_represenation. + Updated parent-child relationships across several categories (ihm_modeling_protocol, ihm_ensemble_info ihm_model_list, ihm_multi_state_modeling, ihm_time_ordered_ensemble, ihm_2dem_class_average_fitting, ihm_cross_link_result) + Updated examples in ihm_dataset_list, ihm_dataset_other and ihm_dataset_related_db_reference + Changed ihm_modeling_experiment to ihm_modeling_protocol to be consistent with the model archive naming convention + Added ihm_sas_restraint category; added _ihm_3dem_restraint.map_segment_flag + Modified the following categories: ihm_model_list, ihm_modeling_protocol, ihm_multi_state_modeling, ihm_time_ordered_ensemble + Minor updates to ihm_cross_link_list, ihm_cross_link_restraint and ihm_model_representation categories. + Added _ihm_sphere_obj_site.rmsf and _ihm_starting_model_details.asym_id + Added ihm_related_datasets and ihm_cross_link_result_parameters + Added _ihm_3dem_restraint.struct_assembly_id, _ihm_sas_restraint.struct_assembly_id, _ihm_starting_model_details.notes and _ihm_starting_model_coord.group_PDB + Changed _ihm_3dem_restraint.id to _ihm_3dem_restraint.ordinal_id and _ihm_sas_restraint.id to _ihm_sas_restraint.ordinal_id + Changed _ihm_dataset_related_db_reference.access_code to _ihm_dataset_related_db_reference.accession_code + Added new categories to reference externally hosted files: IHM_LOCALIZATION_DENSITY_FILES, + IHM_STARTING_MODEL_ALIGNMENT_FILES, IHM_MODELING_WORKFLOW_FILES + Added IHM_DATA_DOI_URL_INFO category to include a URL corresponding to a DOI. This enables automated download of files. + Removed redundant DOI references from several categories + Added _ihm_starting_model_details.starting_model_sequence_offset + Changed _ihm_starting_model_details.starting_model_db_pdb_auth_asym_id to _ihm_starting_model_details.starting_model_auth_asym_id + Changed IHM_DOI_URL_INFO to IHM_EXTERNAL_REFERENCE_INFO; modified all downstream dependencies + Changed IHM_DATASET_OTHER to IHM_DATASET_EXTERNAL_REFERENCE_DETAILS; modified all downstream dependencies + Modified definitions within IHM_EXTERNAL_REFERENCE_INFO + Added IHM_EXTERNAL_FILES category; Removed IHM_STARTING_MODEL_ALIGNMENT_FILES category + Changed IHM_MODELING_WORKFLOW_FILES, IHM_LOCALIZATION_DENSITY_FILES + Changed IHM_DATASET_EXTERNAL_REFERENCE_DETAILS to IHM_DATASET_EXTERNAL_REFERENCE + Modified IHM_STARTING_MODEL_DETAILS category + Added IHM_STARTING_COMPARATIVE_MODELS category + Added IHM_STARTING_MODEL_SEQ_DIF category; removed _ihm_starting_model_details.notes + Updated IHM_ENSEMBLE_INFO, IHM_EXTERNAL_FILES and IHM_EXTERNAL_REFERENCE_INFO + Added _ihm_multi_state_modeling.experiment_type; updated IHM_ENSEMBLE_INFO ; mmcif_ihm-core.dic 0.100 2017-03-23 ; Changes (bv): + Release as provisional version 0.100 + Added _ihm_external_files.content_type + Added _ihm_external_files.details + Removed IHM_MODELING_WORKFLOW_FILES ; mmcif_ihm-core.dic 0.101 2017-03-29 ; Changes (bv): + Updated _ihm_starting_model_seq_dif.db_entity_id as non-mandatory ; mmcif_ihm-core.dic 0.102 2017-03-29 ; Changes (bv): + Updated examples in IHM_STARTING_COMPARATIVE_MODELS ; mmcif_ihm-core.dic 0.103 2017-03-30 ; Changes (bv): + Updated IHM_STARTING_MODEL_DETAILS + Updated IHM_STARTING_COMPARATIVE_MODELS + Updated IHM_DATASET_LIST, IHM_RELATED_DATASETS + Updated IHM_DATASET_RELATED_DB_REFERENCE + Updated IHM_DATASET_EXTERNAL_REFERENCE + Added examples to IHM_EXTERNAL_REFERENCE_INFO and IHM_EXTERNAL_FILES ; mmcif_ihm-core.dic 0.104 2017-04-19 ; Changes (bv): + Updated IHM_STARTING_MODEL_DETAILS + Updated IHM_STARTING_COMPARATIVE_MODELS + Updated IHM_STARTING_MODEL_SEQ_DIF + Updated IHM_MODEL_REPRESENTATION + Updated IHM_DATASET_LIST + Added IHM_DATASET_GROUP + Updated IHM_MODELING_PROTOCOL ; mmcif_ihm-core.dic 0.105 2017-05-25 ; Changes (bv): + Added item description to _ihm_ensemble_info.ensemble_file_id + Added item description to _ihm_2dem_class_average_restraint.pixel_size_width + Added item description to _ihm_2dem_class_average_restraint.pixel_size_height + Added category description to ihm_2dem_class_average_fitting + Added enumeration 'DCD' to _ihm_external_files.file_format + Changed _ihm_external_files.file_size_kb to _ihm_external_files.file_size_bytes ; mmcif_ihm-core.dic 0.106 2017-07-13 ; Changes (bv): + Updated dictionary description and version history ; mmcif_ihm-core.dic 0.107 2017-07-17 ; Changes (ep/bv): + Added category_group_list, item_type_list and item_units_list categories ; mmcif_ihm-core.dic 0.108 2017-09-12 ; Changes (bv): + Added IHM_STRUCT_ASSEMBLY_CLASS, IHM_STRUCT_ASSEMBLY_CLASS_LIST + Added _ihm_struct_assembly.parent_assembly_id ; mmcif_ihm-core.dic 0.109 2017-09-28 ; Changes (bv): + Added _ihm_model_list.representation_id + Added _atom_site.ihm_model_id ; mmcif_ihm-core.dic 0.110 2017-10-03 ; Changes (bv): + Added _ihm_cross_link_restraint.atom_id_1, _ihm_cross_link_restraint.atom_id_2 + Added _ihm_cross_link_restraint.restraint_type + Changed _ihm_cross_link_restraint.type to _ihm_cross_link_restraint.linker_type + Changed _ihm_cross_link_list.type to _ihm_cross_link_list.linker_type + Added enumerations to _ihm_cross_link_restraint.linker_type and _ihm_cross_link_list.linker_type + Added enumeration to and changed _item.mandatory_code of _ihm_cross_link_restraint.model_granularity + Added ihm_predicted_contact_restraint category + Added enumeration to _ihm_dataset_list.data_type ; mmcif_ihm-core.dic 0.111 2017-10-04 ; Changes (bv): + Removed _ihm_cross_link_restraint.linker_type + Updated enumerations to _ihm_cross_link_restraint.restraint_type ; mmcif_ihm-core.dic 0.112 2017-10-04 ; Changes (bv): + Added _ihm_dataset_list.details + Added enumeration to _ihm_dataset_list.data_type ; mmcif_ihm-core.dic 0.113 2017-10-06 ; Changes (bv): + Added IHM_MODEL_REPRESENTATIVE + Added enumeration to _ihm_cross_link_list.linker_type + Updated item description for _ihm_predicted_contact_restraint.probability ; mmcif_ihm-core.dic 0.114 2017-10-09 ; Changes (bv): + Fixed typos and syntax ; mmcif_ihm-core.dic 0.115 2017-10-12 ; Changes (bv): + Added _ihm_modeling_post_process.feature_name + Fixed enumeration for _ihm_cross_link_list.linker_type ; mmcif_ihm-core.dic 0.116 2017-10-16 ; Changes (bv): + Updated _item_description.description for _ihm_model_list.model_group_id + Updated enumerations for _ihm_dataset_list.data_type + Updated parent-child relationships within _ihm_model_list.model_id ; mmcif_ihm-core.dic 0.117 2017-11-09 ; Changes (bv): + Updated description for _ihm_starting_model_details.starting_model_sequence_offset ; mmcif_ihm-core.dic 0.118 2017-12-06 ; Changes (bv): + Changed ihm_time_ordered_ensemble to ihm_ordered_ensemble with appropriate revisions to the category + Changed _ihm_modeling_protocol.time_ordered_flag to _ihm_modeling_protocol.ordered_flag + Changed mandatory code for _ihm_model_list.representation_id + Added an example to ihm_model_list category ; mmcif_ihm-core.dic 0.119 2017-12-07 ; Changes (bv): + Changed ihm_ordered_ensemble.ordered_process_id to ihm_ordered_ensemble.process_id + Changed ihm_ordered_ensemble.ordered_process_description to ihm_ordered_ensemble.process_description. + Changed parent-child relationships for _ihm_predicted_contact_restraint.atom_id_1, _ihm_predicted_contact_restraint.atom_id_2, _ihm_cross_link_restraint.atom_id_1, _ihm_cross_link_restraint.atom_id_2, _ihm_starting_model_coord.atom_id ; mmcif_ihm-core.dic 0.120 2018-01-10 ; Changes (bv): + Added ihm_feature_selection_atom, ihm_feature_selection_residue, ihm_derived_distance_restraint + Fixed typos in the parent name of _ihm_predicted_contact_restraint.atom_id_1 and _ihm_predicted_contact_restraint.atom_id_2 + Fixed _item_type.code in _ihm_starting_model_coord.atom_id ; mmcif_ihm-core.dic 0.121 2018-01-17 ; Changes (bv): + Added _ihm_derived_distance_restraint.distance_upper_limit_std and _ihm_derived_distance_restraint.distance_lower_limit_std + Updated _item_type.code for _ihm_external_reference_info.reference_type and _ihm_external_reference_info.reference_provider ; mmcif_ihm-core.dic 0.122 2018-01-22 ; Changes (bv): + Updated parent-child relationships for _ihm_model_representation.entity_id, _ihm_struct_assembly.entity_id, _ihm_feature_selection_atom.entity_id, _ihm_feature_selection_residue.entity_id + Changed _ihm_derived_distance_restraint.distance_lower_limit_std to _ihm_derived_distance_restraint.distance_lower_limit_esd + Changed _ihm_derived_distance_restraint.distance_upper_limit_std to _ihm_derived_distance_restraint.distance_upper_limit_esd + Added enumeration for _ihm_external_reference_info.refers_to and _ihm_external_files.file_format ; mmcif_ihm-core.dic 0.123 2018-01-24 ; Changes (bv): + Added IHM_STRUCT_ASSEMBLY_DETAILS category. + Updated parent-child relationships for _ihm_starting_model_details.entity_description, _ihm_model_representation.entity_description, _ihm_struct_assembly.entity_description, _ihm_predicted_contact_restraint.entity_description_1, _ihm_cross_link_list.entity_description_1, _ihm_predicted_contact_restraint.entity_description_2, _ihm_cross_link_list.entity_description_2 ; mmcif_ihm-core.dic 0.124 2018-02-01 ; Changes (bv): + Updated parent-child relationships for _ihm_model_representation.entity_id, _ihm_struct_assembly.entity_id + Added IHM_FEATURE_LIST and IHM_NON_POLY_ATOM_FEATURE categories. + Changed IHM_FEATUTE_SELECTION_ATOM to IHM_POLY_ATOM_FEATURE. + Changed IHM_FEATUTE_SELECTION_RESDIUE to IHM_POLY_RESIDUE_FEATURE. + Updated IHM_DERIVED_DISTANCE_RESTRAINT ; mmcif_ihm-core.dic 0.125 2018-02-05 ; Changes (bv): + Added _ihm_derived_distance_restraint.random_exclusion_fraction + Changed _ihm_derived_distance_restraint.conditionality to _ihm_derived_distance_restraint.group_conditionality + Updated description for _ihm_derived_distance_restraint.group_conditionality ; mmcif_ihm-core.dic 0.126 2018-02-06 ; Changes (bv): + Updated enumeration list for _ihm_dataset_list.data_type ; mmcif_ihm-core.dic 0.127 2018-02-26 ; Changes (bv): + Added _ihm_poly_residue_feature.residue_range_granularity, _ihm_poly_residue_feature.rep_atom + Updated enumeration for _ihm_cross_link_list.linker_type, _ihm_external_files.content_type ; mmcif_ihm-core.dic 0.128 2018-03-16 ; Changes (bv): + Added _ihm_dataset_group.application and _ihm_dataset_group.details + Updated enumeration for _ihm_modeling_post_process.type + Fixed typos ; mmcif_ihm-core.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-core.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-core.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-core.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-core.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-core.dic 0.134 2018-07-18 ; Changes (bv): + Updated _item_sub_category.id for matrices and vectors ; mmcif_ihm-core.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-core.dic 0.136 2018-10-05 ; Changes (bv): + Added ihm_hydroxyl_radical_fp_restraint ; mmcif_ihm-core.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-core.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-core.dic 0.139 2019-01-03 ; Changes (bv): + Changed IHM_FEATURE_PSEUDO_SITE to IHM_PSEUDO_SITE_FEATURE ; mmcif_ihm-core.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-core.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-core.dic 1.0 2019-05-31 ; Changes (bv): + Updated several categories to fix primary key information and parent-child relationships ; mmcif_ihm-core.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-core.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-core.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-core.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-core.dic 1.05 2019-11-15 ; Changes (bv): + Added BMSO and DHSO to _ihm_cross_link_list.linker_type enumeration list ; mmcif_ihm-core.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-core.dic 1.07 2020-02-10 ; Changes (bv): + Added CYS to _ihm_cross_link_list.linker_type enumeration list ; mmcif_ihm-core.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-core.dic 1.09 2020-03-19 ; Changes (bv): + Added ihm_data_transformation + Added _ihm_related_datasets.transformation_id ; mmcif_ihm-core.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-core.dic 1.11 2020-07-03 ; Changes (bv): + Added ihm_hdx_restraint ; mmcif_ihm-core.dic 1.12 2020-07-10 ; Changes (bv): + Added enumerations to _ihm_cross_link_list.linker_type ; mmcif_ihm-core.dic 1.13 2021-01-28 ; Changes (bv): + Added enumerations to _ihm_cross_link_list.linker_type ; mmcif_ihm-core.dic 1.14 2021-03-04 ; Changes (bv): + Added enumerations to _ihm_cross_link_list.linker_type ; mmcif_ihm-core.dic 1.15 2021-03-16 ; Changes (bv): + Added enumerations to _ihm_dataset_related_db_reference.db_name ; mmcif_ihm-core.dic 1.16 2021-04-14 ; Changes (bv): + Added enumerations to _ihm_cross_link_list.linker_type ; mmcif_ihm-core.dic 1.17 2021-05-21 ; Changes (bv): + Added enumerations to _ihm_cross_link_list.linker_type ; mmcif_ihm-core.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-core.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-core.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-core.dic 1.21 2023-03-24 ; Changes (bv): + Added enumerations to _ihm_cross_link_list.linker_type ; mmcif_ihm-core.dic 1.22 2023-05-26 ; Changes (bv): + Added enumerations to _ihm_dataset_related_db_reference.db_name ; mmcif_ihm-core.dic 1.23 2023-07-05 ; Changes (bv): + Added enumerations to _ihm_cross_link_list.linker_type ; mmcif_ihm-core.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-core.dic 1.25 2023-12-22 ; + Rename dictionary + Reorganize repository ; # loop_ _sub_category.id _sub_category.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. ; 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. ; 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. ; 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. ; 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. ; vector " The collection of elements of a vector." unit_vector " The collection of elements of a vector whose norm equals 1." 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. ; mm_poly_res_label " The collection of entity id, comp id and seq id components of the label for a residue in a polymer." # loop_ _category_group_list.id _category_group_list.parent_id _category_group_list.description inclusive_group . " The parent category group containing all of the data categories in the macromolecular dictionary." atom_group inclusive_group " Categories that describe the properties of atoms." array_data_group inclusive_group " Categories that describe array data." axis_group inclusive_group " Categories that describe axes." audit_group inclusive_group ; Categories that describe dictionary maintenance and identification. ; cell_group inclusive_group " Categories that describe the unit cell." chemical_group inclusive_group " Categories that describe chemical features derived from the experimental coordinate data." chem_comp_group inclusive_group " Categories that define the chemical structure and nomenclature of the momoners and ligands in the experiment." chem_comp_dictionary_group inclusive_group ; Categories defining chemical structure and nomenclature of the momoners and ligands used in the Chemical Component Dictionary. ; chem_comp_model_group inclusive_group " Categories defining structural models for chemical components defined in the Chemical Component Dictionary." bird_dictionary_group inclusive_group ; Categories defining chemical structure and nomenclature of the small polymer molecules used in the Biologically Interesting Molecule Reference Dictionary (BIRD). ; bird_family_dictionary_group inclusive_group " Categories defining families of related molecules used in the Biologically Interesting Molecule Reference Dictionary (BIRD)." chem_link_group inclusive_group ; Categories that describe links between components of chemical structure. ; citation_group inclusive_group " Categories that provide bibliographic references." computing_group inclusive_group " Categories that describe the computational details of the experiment." compliance_group inclusive_group ; Categories that are included in this dictionary specifically to comply with previous dictionaries. ; database_group inclusive_group ; Categories that hold references to entries in databases that contain related information. ; diffrn_group inclusive_group " Categories that describe details of the diffraction experiment." em_group inclusive_group " Categories that describe 3-dimensional electron microscopy." em_legacy_group inclusive_group " Categories that describe 3-dimensional electron microscopy (legacy)." emdb_admin_group inclusive_group " Administrative Categories for Electron Microscopy Data Bank." emdb_extension_group inclusive_group " Categories that describe 3-dimensional electron microscopy (EMDB extension)." entity_group inclusive_group " Categories that describe the unique chemical and molecular entities." entry_group inclusive_group " Categories that pertain to the entire data block." exptl_group inclusive_group " Categories that hold details of the experimental conditions." geom_group inclusive_group " Categories that hold details of molecular and crystal geometry." iucr_group inclusive_group ; Categories that are used for manuscript submission and internal processing by the staff of the International Union of Crystallography. ; nmr_group inclusive_group " Categories that describe Nuclear Magnetic Spectroscopy experiments." pdb_group inclusive_group ; Categories that pertain to the file-format or data-processing codes used by the Protein Data Bank. ; phasing_group inclusive_group " Categories that describe phasing." refine_group inclusive_group " Categories that describe refinement." refln_group inclusive_group " Categories that describe the details of reflection measurements." struct_group inclusive_group " Categories that contain details about the experimental structure." symmetry_group inclusive_group " Categories that describe symmetry information." pdbx_group inclusive_group " Categories which have been added to support the data archiving and exchange for the Protein Data Bank." pdbx_erf_group inclusive_group ; Categories which are used by RCSB PDB to store derived and computed data. ; ccp4_group inclusive_group " Categories from the CCP4 harvest dictionary." ndb_group inclusive_group " Categories which are used by the Nucleic Acid Database." rcsb_group inclusive_group " Categories which are used internally by the RCSB PDB." protein_production_group inclusive_group " Categories which describe the details of protein production." solution_scattering_group inclusive_group " Categories which describe the details of solution scattering experiments." validate_group inclusive_group ; Categories that describe geometric properties of residues that deviate from expected standards by 6 * the expected RMSD ; view_group inclusive_group " Categories which are used to storing view transformations." em_specimen inclusive_group " Categories that describe electron microscopy specimens." em_sample inclusive_group " Categories that describe electron microscopy samples." em_crystallography inclusive_group " Categories that describe electron crystallography." em_fitting inclusive_group " Categories that describe electron microscopy fitting." em_tomography inclusive_group " Categories that describe electron tomography." em_imaging inclusive_group " Categories that describe electron microscopy imaging." em_reconstruction inclusive_group " Categories that describe electron microscopy reconstruction." em_symmetry_group inclusive_group " Categories that describe electron microscopy symmetry." em_experiment inclusive_group " Categories that describe electron microscopy experimental details." em_symmetry inclusive_group " Categories that describe electron microscopy symmetry details." emd_group inclusive_group " Categories describing electron microscopy that are used by the wwPDB deposition and annotation system." chem_comp_model_group inclusive_group " Categories describing experimental and computational models for individual chemical components." dcc_group inclusive_group " Categories output by the crystallographic data utility application DCC." xfel_group inclusive_group " Categories that describe X-ray Free Electron Laser (XFEL) data collection and experimental details." diffrn_data_set_group inclusive_group " Categories extending the description of measured diffraction data." branch_group inclusive_group " Categories that describe branched chain carbohydrates." reference_sequence_group inclusive_group " Categories that describe SIFTS mapping of sequence data." ihm_group inclusive_group " Categories that describe the integrative/hybrid methods extension dictionary (IHMCIF)." # loop_ _item_type_list.code _item_type_list.primitive_code _item_type_list.construct _item_type_list.detail code char ;[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* ; " code item types/single words ..." ucode uchar ;[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* ; " code item types/single words (case insensitive) ..." line char ;[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* ; " char item types / multi-word items ..." uline uchar ;[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* ; " char item types / multi-word items (case insensitive)..." text char ;[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* ; " text item types / multi-line text ..." int numb "[+-]?[0-9]+" ; int item types are the subset of numbers that are the negative or positive integers. ; float numb -?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? ; float item types are the subset of numbers that are the floating numbers. ; name uchar "_[_A-Za-z0-9]+\.[][_A-Za-z0-9%-]+" " name item types take the form..." idname uchar "[_A-Za-z0-9]+" " idname item types take the form..." any char .* " A catch all for items that may take any form..." yyyy-mm-dd char "[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]" ; Standard format for CIF dates. ; yyyy-mm-dd:hh:mm-flex char "[0-9][0-9][0-9][0-9](-[0-9]?[0-9])?(-[0-9][0-9])?(:[0-9]?[0-9]:[0-9][0-9])?" ; Flexible date-time format. ; uchar3 uchar "[+]?[A-Za-z0-9][A-Za-z0-9]?[A-Za-z0-9]?" ; data item for 3 character codes ; uchar5 uchar "[+]?[A-Za-z0-9][A-Za-z0-9]?[A-Za-z0-9]?[A-Za-z0-9]?[A-Za-z0-9]?" ; data item for 5 character codes ; uchar1 uchar "[+]?[A-Za-z0-9]" ; data item for 1 character codes ; symop char ([1-9]|[1-9][0-9]|1[0-8][0-9]|19[0-2])(_[1-9][1-9][1-9])? ; symop item types take the form n_klm, where n refers to the symmetry operation that is applied to the coordinates in the ATOM_SITE category identified by _atom_site_label. It must match a number given in _symmetry_equiv_pos_site_id. k, l, and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used. These translations (x,y,z) are related to (k,l,m) by k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; atcode char ;[][ _(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* ; " Character data type for atom names ..." 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. ; fax uchar ;[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* ; " code item types/single words (case insensitive) ..." phone uchar ;[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* ; " code item types/single words (case insensitive) ..." email uchar ;[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* ; " code item types/single words (case insensitive) ..." int-range numb "[+-]?[0-9]+-[+-]?[0-9]+" ; range of integer item types are the subset of numbers that are the negative or positive integers. ; float-range numb -?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?(--?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?)? ; int item types are the subset of numbers that are the floating numbers. ; code30 char .?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.? "A string value, not allowed to exceed 30 characters." binary char ;\n--CIF-BINARY-FORMAT-SECTION--\n\ [][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*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. ; operation_expression char ;[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* ; " sequence of parenthetical integer ranges and character codes" 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. ; 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" ucode-alphanum-csv uchar "[A-Za-z0-9]+(,[A-Za-z0-9]+)?" " comma separated alpha numeric codes (single words) (case insensitive) ..." 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." asym_id char "[A-Za-z0-9]+" " A single chain or asym ids." 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." 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. ; pdbx_related_db_id char ;[][_.:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* ; " code item types/single words without semi-colon or comma ..." 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" positive_int numb "[1-9][0-9]*" "Positive integers (1,2,3,..)" emd_id char EMD-[0-9]{4,} "EMDB code" 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)" 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" boolean char YES|NO "Boolean type" 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." 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" 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" sequence_dep char "[a-zA-Z0-9\t \r\n\v\f\(\)]+$" "Deposition specific one letter code" 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" citation_doi char 10\..* "Citation DOI specification." exp_data_doi char 10\.[0-9]{4,9}/[-._;()/:A-Za-z0-9]+ "Experimental dataset DOI" deposition_email uchar "[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9.-]+" "code item types/single words (case insensitive) ..." # loop_ _item_units_list.code _item_units_list.detail metres "metres (metres)" centimetres "centimetres (metres * 10^( -2)^)" millimetres "millimetres (metres * 10^( -3)^)" micrometres "micrometres (metres * 10^( -6)^)" nanometres "nanometres (metres * 10^( -9)^)" nanometers "nanometers (metres * 10^( -9)^)" angstroms "angstroms (metres * 10^(-10)^)" picometres "picometres (metres * 10^(-12)^)" femtometres "femtometres (metres * 10^(-15)^)" reciprocal_metres "reciprocal metres (metres^(-1)^)" reciprocal_centimetres "reciprocal centimetres ((metres * 10^( -2))^(-1))" reciprocal_millimetres "reciprocal millimetres ((metres * 10^( -3)^)^(-1)^)" reciprocal_nanometres "reciprocal nanometres ((metres * 10^( -9)^)^(-1)^)" reciprocal_angstroms "reciprocal angstroms ((metres * 10^(-10)^)^(-1)^)" reciprocal_picometres "reciprocal picometres ((metres * 10^(-12)^)^(-1)^)" micrometres_squared "micrometres squared (metres * 10^( -6)^)^2^" nanometres_squared "nanometres squared (metres * 10^( -9)^)^2^" angstroms_squared "angstroms squared (metres * 10^(-10)^)^2^" 8pi2_angstroms_squared "8pi^2^ * angstroms squared (metres * 10^(-10)^)^2^" picometres_squared "picometres squared (metres * 10^(-12)^)^2^" nanometres_cubed "nanometres cubed (metres * 10^( -9)^)^3^" angstroms_cubed "angstroms cubed (metres * 10^(-10)^)^3^" picometres_cubed "picometres cubed (metres * 10^(-12)^)^3^" kilopascals kilopascals gigapascals gigapascals hours hours minutes minutes seconds seconds microseconds "microseconds (seconds * 10^( -6)^)" femtoseconds "femtoseconds (seconds * 10^( -15)^)" degrees "degrees (of arc)" milliradians "milliradians (of arc)" degrees_per_minute "degrees (of arc) per minute" celsius "degrees (of temperature) Celsius" kelvins "temperature in Kelvin" electrons electrons electrons_squared "electrons squared" electrons_per_nanometres_cubed " electrons per nanometres cubed (electrons/(metres * 10^( -9)^)^(-3)^)" electrons_per_angstroms_cubed " electrons per angstroms cubed (electrons/(metres * 10^(-10)^)^(-3)^)" electrons_per_picometres_cubed " electrons per picometres cubed (electrons/(metres * 10^(-12)^)^(-3)^)" ions_per_cm_squared_per_sec " ions per centimetre squared per second (ions/(meters * 10^(-2)^)^(-2)/second^)" kilowatts kilowatts milliamperes milliamperes kilovolts kilovolts volts volts arbitrary " arbitrary system of units." angstroms_degrees "angstroms * degrees" degrees_squared "degrees squared" mg_per_ml "milliliter per milligram" ml_per_min "milliliters per minute" microliters_per_min "microliters per minute" milliliters "liter / 1000" milligrams "grams / 1000" megadaltons megadaltons kilodaltons kilodaltons kilodaltons/nanometer kilodaltons/nanometer microns_squared "micrometres squared (metres * 10^( -6)^)^2^" microns "micrometres (metres * 10^( -6)^)" electrons_angstrom_squared "electrons square angstrom" electron_volts "electron volts" kiloelectron_volts "KeV (electron volts * 10^( 3)^)" millimolar millimolar megagrams_per_cubic_metre "megagrams per cubic metre" pixels_per_millimetre "pixels per millimetre" counts counts counts_per_photon "counts per photon" pascals pascals teraphotons_per_pulse "(photons * 10^( 12)^) per pulse" joules Joules microjoules "joules * 10^( -6)^" hertz "reciprocal seconds" reciprocal_seconds "reciprocal seconds (seconds^(-1)^)" nanoseconds "nanoseconds (seconds * 10^( -9)^)" # loop_ _item_units_conversion.from_code _item_units_conversion.to_code _item_units_conversion.operator _item_units_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 # loop_ _pdbx_comparison_operator_list.code _pdbx_comparison_operator_list.description = Equal >= "greater or equal" != "Not equal" < "Less than" not_set "If not set" true "Always true" # loop_ _pdbx_conditional_context_list.ordinal_id _pdbx_conditional_context_list.context_id _pdbx_conditional_context_list.target_item_name _pdbx_conditional_context_list.target_item_value _pdbx_conditional_context_list.cmp_op _pdbx_conditional_context_list.log_op 1 WWPDB_NOT_ACCEPT_GDPR_20210924 "_pdbx_database_status.date_accepted_terms_and_conditions" ? not_set ? 2 WWPDB_NOT_ACCEPT_GDPR_20210924 "_pdbx_database_status.date_accepted_terms_and_conditions" 2021-09-24 < or 3 WWPDB_NOT_PI "_pdbx_contact_author.role" ? not_set ? 4 WWPDB_NOT_PI "_pdbx_contact_author.role" "principal investigator/group leader" != or 5 WWPDB_ALWAYS_SUPPRESS "_pdbx_contact_author.role" ? true ? ## save__entity_poly_seq.entity_id _item_description.description ; This data item is a pointer to _entity_poly.entity_id in the ENTITY_POLY category. ; # _item.name "_entity_poly_seq.entity_id" _item.category_id entity_poly_seq _item.mandatory_code yes # _item_type.code code # _item_sub_category.id mm_poly_res_label # _item_linked.child_name "_entity_poly_seq.entity_id" _item_linked.parent_name "_entity_poly.entity_id" # save_ # save__entity_poly_seq.mon_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; # _item.name "_entity_poly_seq.mon_id" _item.category_id entity_poly_seq _item.mandatory_code yes # _item_type.code ucode # _item_sub_category.id mm_poly_res_label # _item_linked.child_name "_entity_poly_seq.mon_id" _item_linked.parent_name "_chem_comp.id" # save_ # save__entity_poly_seq.num _item_description.description ; The value of _entity_poly_seq.num must uniquely and sequentially identify a record in the ENTITY_POLY_SEQ list. Note that this item must be a number and that the sequence numbers must progress in increasing numerical order. ; # _item.name "_entity_poly_seq.num" _item.category_id entity_poly_seq _item.mandatory_code yes # loop_ _item_range.maximum _item_range.minimum . 1 1 1 # _item_type.code int # _item_sub_category.id mm_poly_res_label # save_ # save__entity_poly_seq.hetero _item_description.description ; A flag to indicate whether this monomer in the polymer is heterogeneous in sequence. ; # _item.name "_entity_poly_seq.hetero" _item.category_id entity_poly_seq _item.mandatory_code no # _item_default.value no # _item_type.code ucode # loop_ _item_enumeration.value _item_enumeration.detail no "sequence is not heterogeneous at this monomer" n 'abbreviation for "no"' yes "sequence is heterogeneous at this monomer" y 'abbreviation for "yes"' # save_ # save_ihm_entity_poly_segment _category.description ; Data items in the IHM_ENTITY_POLY_SEGMENT category identifies segments of polymeric entities. ; _category.id ihm_entity_poly_segment _category.mandatory_code no # _category_key.name "_ihm_entity_poly_segment.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_entity_poly_segment.id _ihm_entity_poly_segment.entity_id _ihm_entity_poly_segment.seq_id_begin _ihm_entity_poly_segment.seq_id_end _ihm_entity_poly_segment.comp_id_begin _ihm_entity_poly_segment.comp_id_end 1 1 1 6 MET THR 2 1 7 20 TYR LYS 3 1 21 26 GLU GLN 4 1 27 80 ASN LEU 5 1 81 95 LEU GLU 6 1 96 126 LEU LEU 7 1 127 135 LYS ARG # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_entity_poly_segment # save_ # save__ihm_entity_poly_segment.id _item_description.description " A unique identifier for the polymeric segment." # _item.name "_ihm_entity_poly_segment.id" _item.category_id ihm_entity_poly_segment _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_entity_poly_segment.entity_id _item_description.description ; A unique identifier for the polymeric entity. This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_entity_poly_segment.entity_id" _item.category_id ihm_entity_poly_segment _item.mandatory_code yes # _item_type.code code # loop_ _item_sub_category.id _item_sub_category.pdbx_label mm_poly_res_label mm_poly_res_label_begin mm_poly_res_label mm_poly_res_label_end # _item_linked.child_name "_ihm_entity_poly_segment.entity_id" _item_linked.parent_name "_entity_poly_seq.entity_id" # save_ # save__ihm_entity_poly_segment.seq_id_begin _item_description.description ; The leading residue index for the polymeric segment. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_entity_poly_segment.seq_id_begin" _item.category_id ihm_entity_poly_segment _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_begin # _item_linked.child_name "_ihm_entity_poly_segment.seq_id_begin" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_entity_poly_segment.seq_id_end _item_description.description ; The trailing residue index for the polymeric segment. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_entity_poly_segment.seq_id_end" _item.category_id ihm_entity_poly_segment _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_end # _item_linked.child_name "_ihm_entity_poly_segment.seq_id_end" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_entity_poly_segment.comp_id_begin _item_description.description ; The leading monomer component of the polymeric segment. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_entity_poly_segment.comp_id_begin" _item.category_id ihm_entity_poly_segment _item.mandatory_code yes # _item_type.code ucode # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_begin # _item_linked.child_name "_ihm_entity_poly_segment.comp_id_begin" _item_linked.parent_name "_entity_poly_seq.mon_id" # save_ # save__ihm_entity_poly_segment.comp_id_end _item_description.description ; The trailing monomer component of the polymeric segment. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_entity_poly_segment.comp_id_end" _item.category_id ihm_entity_poly_segment _item.mandatory_code yes # _item_type.code ucode # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_end # _item_linked.child_name "_ihm_entity_poly_segment.comp_id_end" _item_linked.parent_name "_entity_poly_seq.mon_id" # save_ # save_ihm_starting_model_details _category.description ; Data items in the IHM_STARTING_MODEL_DETAILS category records the details about structural models used as starting inputs in the integrative model building process. ; _category.id ihm_starting_model_details _category.mandatory_code no # _category_key.name "_ihm_starting_model_details.starting_model_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_starting_model_details.starting_model_id _ihm_starting_model_details.entity_id _ihm_starting_model_details.entity_description _ihm_starting_model_details.asym_id _ihm_starting_model_details.entity_poly_segment_id _ihm_starting_model_details.starting_model_source _ihm_starting_model_details.starting_model_auth_asym_id _ihm_starting_model_details.starting_model_sequence_offset _ihm_starting_model_details.dataset_list_id Nup84-m1 1 Nup84 A 1 'comparative model' A 0 5 Nup85-m1 2 Nup85 B 2 'comparative model' B 0 9 Nup120-m1 3 Nup120 C 3 'comparative model' C 0 13 Nup133-m1 4 Nup133 D 4 'comparative model' D 0 15 Nup133-m2 4 Nup133 D 4 'comparative model' D 0 16 Nup145c-m1 5 Nup145c E 5 'comparative model' E 0 19 Seh1-m1 6 Seh1 F 6 'experimental model' A 0 20 Sec13-m1 7 Sec13 G 7 'experimental model' D 0 21 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_starting_model_details # save_ # save__ihm_starting_model_details.starting_model_id _item_description.description " A unique identifier for the starting structural model." # _item.name "_ihm_starting_model_details.starting_model_id" _item.category_id ihm_starting_model_details _item.mandatory_code yes # _item_type.code code # save_ # save__ihm_starting_model_details.entity_id _item_description.description ; A unique identifier for the distinct molecular entities. This data item is a pointer to _entity.id in the ENTITY category. ; # _item.name "_ihm_starting_model_details.entity_id" _item.category_id ihm_starting_model_details _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_starting_model_details.entity_id" _item_linked.parent_name "_entity.id" # save_ # save__ihm_starting_model_details.entity_description _item_description.description ; A text description of the molecular entity ; # _item.name "_ihm_starting_model_details.entity_description" _item.category_id ihm_starting_model_details _item.mandatory_code no # _item_type.code line # save_ # save__ihm_starting_model_details.asym_id _item_description.description ; An asym/strand identifier for the entity molecule. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_starting_model_details.asym_id" _item.category_id ihm_starting_model_details _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_starting_model_details.asym_id" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_starting_model_details.entity_poly_segment_id _item_description.description ; The identifier for the polymeric segment modeled using this starting model. This data item is a pointer to _ihm_entity_poly_segment.id in the IHM_ENTITY_POLY_SEGMENT category. ; # _item.name "_ihm_starting_model_details.entity_poly_segment_id" _item.category_id ihm_starting_model_details _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_starting_model_details.entity_poly_segment_id" _item_linked.parent_name "_ihm_entity_poly_segment.id" # save_ # save__ihm_starting_model_details.starting_model_source _item_description.description " The source of the starting model." # _item.name "_ihm_starting_model_details.starting_model_source" _item.category_id ihm_starting_model_details _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail "comparative model" . "experimental model" . "integrative model" . "ab initio model" . other . # save_ # save__ihm_starting_model_details.starting_model_auth_asym_id _item_description.description ; The author assigned chainId/auth_asym_id corresponding to this starting model. This corresponds to the chainId/auth_asym_id of the experimental models in the PDB or comparative models in the Model Archive or the starting models referenced via a DOI. If starting models are included in IHM_STARTING_MODEL_COORD, then this will be the same as _ihm_starting_model_details.asym_id. ; # _item.name "_ihm_starting_model_details.starting_model_auth_asym_id" _item.category_id ihm_starting_model_details _item.mandatory_code yes # _item_type.code code # save_ # save__ihm_starting_model_details.starting_model_sequence_offset _item_description.description ; The offset in residue numbering between the starting model and the deposited I/H model, if applicable. I/H model residue number = Starting model residue number + offset ; # _item.name "_ihm_starting_model_details.starting_model_sequence_offset" _item.category_id ihm_starting_model_details _item.mandatory_code no # _item_type.code int # save_ # save__ihm_starting_model_details.dataset_list_id _item_description.description ; Identifier to the starting model (comparative, experimental or integrative) used as input in the integrative modeling. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_starting_model_details.dataset_list_id" _item.category_id ihm_starting_model_details _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_starting_model_details.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save__ihm_starting_model_details.description _item_description.description " Additional description regarding the starting model." # _item.name "_ihm_starting_model_details.description" _item.category_id ihm_starting_model_details _item.mandatory_code no # _item_type.code text # save_ # save_ihm_starting_comparative_models _category.description ; Data items in the IHM_STARTING_COMPARATIVE_MODELS category records additional details about comparative models used as starting inputs in the integrative model building process. ; _category.id ihm_starting_comparative_models _category.mandatory_code no # _category_key.name "_ihm_starting_comparative_models.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_starting_comparative_models.id _ihm_starting_comparative_models.starting_model_id _ihm_starting_comparative_models.starting_model_auth_asym_id _ihm_starting_comparative_models.starting_model_seq_id_begin _ihm_starting_comparative_models.starting_model_seq_id_end _ihm_starting_comparative_models.template_auth_asym_id _ihm_starting_comparative_models.template_seq_id_begin _ihm_starting_comparative_models.template_seq_id_end _ihm_starting_comparative_models.template_sequence_identity _ihm_starting_comparative_models.template_sequence_identity_denominator _ihm_starting_comparative_models.template_dataset_list_id _ihm_starting_comparative_models.alignment_file_id 3 Nup84-m1 A 429 488 G 482 551 10.0 1 3 7 4 Nup84-m1 A 506 726 A 667 913 17.6 1 2 6 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_starting_comparative_models # save_ # save__ihm_starting_comparative_models.id _item_description.description " A unique identifier for the starting comparative model." # _item.name "_ihm_starting_comparative_models.id" _item.category_id ihm_starting_comparative_models _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_starting_comparative_models.starting_model_id _item_description.description ; The identifier for the starting structural model. This data item is a pointer to _ihm_starting_model_details.starting_model_id in the IHM_STARTING_MODEL_DETAILS category. ; # _item.name "_ihm_starting_comparative_models.starting_model_id" _item.category_id ihm_starting_comparative_models _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_starting_comparative_models.starting_model_id" _item_linked.parent_name "_ihm_starting_model_details.starting_model_id" # save_ # save__ihm_starting_comparative_models.starting_model_auth_asym_id _item_description.description " The chainId/auth_asym_id corresponding to the starting model." # _item.name "_ihm_starting_comparative_models.starting_model_auth_asym_id" _item.category_id ihm_starting_comparative_models _item.mandatory_code yes # _item_type.code code # save_ # save__ihm_starting_comparative_models.starting_model_seq_id_begin _item_description.description " The starting residue index of the starting model." # _item.name "_ihm_starting_comparative_models.starting_model_seq_id_begin" _item.category_id ihm_starting_comparative_models _item.mandatory_code no # _item_type.code int # save_ # save__ihm_starting_comparative_models.starting_model_seq_id_end _item_description.description " The ending residue index of the starting model." # _item.name "_ihm_starting_comparative_models.starting_model_seq_id_end" _item.category_id ihm_starting_comparative_models _item.mandatory_code no # _item_type.code int # save_ # save__ihm_starting_comparative_models.template_auth_asym_id _item_description.description " The chainId/auth_asym_id corresponding to the template." # _item.name "_ihm_starting_comparative_models.template_auth_asym_id" _item.category_id ihm_starting_comparative_models _item.mandatory_code yes # _item_type.code code # save_ # save__ihm_starting_comparative_models.template_seq_id_begin _item_description.description " The starting residue index of the template." # _item.name "_ihm_starting_comparative_models.template_seq_id_begin" _item.category_id ihm_starting_comparative_models _item.mandatory_code no # _item_type.code int # save_ # save__ihm_starting_comparative_models.template_seq_id_end _item_description.description " The ending residue index of the template." # _item.name "_ihm_starting_comparative_models.template_seq_id_end" _item.category_id ihm_starting_comparative_models _item.mandatory_code no # _item_type.code int # save_ # save__ihm_starting_comparative_models.template_sequence_identity _item_description.description " The percentage sequence identity between the template sequence and the comparative model sequence." # _item.name "_ihm_starting_comparative_models.template_sequence_identity" _item.category_id ihm_starting_comparative_models _item.mandatory_code no # _item_type.code float # save_ # save__ihm_starting_comparative_models.template_sequence_identity_denominator _item_description.description ; The denominator used while calculating the sequence identity provided in _ihm_starting_comparative_models.template_sequence_identity. ; # _item.name "_ihm_starting_comparative_models.template_sequence_identity_denominator" _item.category_id ihm_starting_comparative_models _item.mandatory_code no # _item_type.code int # _item_dependent.dependent_name "_ihm_starting_comparative_models.template_sequence_identity" # loop_ _item_enumeration.value _item_enumeration.detail 1 "Length of the shorter sequence" 2 "Number of aligned positions (including gaps)" 3 "Number of aligned residue pairs (not including the gaps)" 4 "Arithmetic mean sequence length" 5 Other # save_ # save__ihm_starting_comparative_models.template_dataset_list_id _item_description.description ; The dataset list id corresponding to the template used to obtain the comparative model. This data item is a pointer to _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_starting_comparative_models.template_dataset_list_id" _item.category_id ihm_starting_comparative_models _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_starting_comparative_models.template_dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save__ihm_starting_comparative_models.alignment_file_id _item_description.description ; The file id corresponding to the sequence alignment of the template sequence and the comparative model sequence. This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES category. ; # _item.name "_ihm_starting_comparative_models.alignment_file_id" _item.category_id ihm_starting_comparative_models _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_starting_comparative_models.alignment_file_id" _item_linked.parent_name "_ihm_external_files.id" # save_ # save__ihm_starting_comparative_models.details _item_description.description " Additional details regarding the starting comparative models." # _item.name "_ihm_starting_comparative_models.details" _item.category_id ihm_starting_comparative_models _item.mandatory_code no # _item_type.code text # save_ # save_ihm_starting_computational_models _category.description ; Data items in the IHM_STARTING_COMPUTATIONAL_MODELS category records additional details about computational models used as starting inputs in the integrative model building process. ; _category.id ihm_starting_computational_models _category.mandatory_code no # _category_key.name "_ihm_starting_computational_models.starting_model_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_starting_computational_models.starting_model_id _ihm_starting_computational_models.script_file_id _ihm_starting_computational_models.software_id 1 8 2 2 9 2 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_starting_computational_models # save_ # save__ihm_starting_computational_models.starting_model_id _item_description.description ; The identifier for the starting structural model. This data item is a pointer to _ihm_starting_model_details.starting_model_id in the IHM_STARTING_MODEL_DETAILS category. ; # _item.name "_ihm_starting_computational_models.starting_model_id" _item.category_id ihm_starting_computational_models _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_starting_computational_models.starting_model_id" _item_linked.parent_name "_ihm_starting_model_details.starting_model_id" # save_ # save__ihm_starting_computational_models.script_file_id _item_description.description ; The file id corresponding to the script used in the computational modeling. This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES category. ; # _item.name "_ihm_starting_computational_models.script_file_id" _item.category_id ihm_starting_computational_models _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_starting_computational_models.script_file_id" _item_linked.parent_name "_ihm_external_files.id" # save_ # save__ihm_starting_computational_models.software_id _item_description.description ; An identifier to the software used in computational modeling. This data item is a pointer to _software.pdbx_ordinal in the SOFTWARE category. ; # _item.name "_ihm_starting_computational_models.software_id" _item.category_id ihm_starting_computational_models _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_starting_computational_models.software_id" _item_linked.parent_name "_software.pdbx_ordinal" # save_ # save_ihm_starting_model_seq_dif _category.description ; Data items in the IHM_STARTING_MODEL_SEQ_DIF category provide a mechanism for indicating and annotating point differences between the sequence of the entity or biological unit described in the data block and the sequence of the starting model used in the integrative modeling referenced from a database. The point differences may be due to point mutations introduced in the starting model or the presence of modified amino acid residues. ; _category.id ihm_starting_model_seq_dif _category.mandatory_code no # _category_key.name "_ihm_starting_model_seq_dif.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 ; _category_examples.case ; loop_ _ihm_starting_model_seq_dif.id _ihm_starting_model_seq_dif.entity_id _ihm_starting_model_seq_dif.asym_id _ihm_starting_model_seq_dif.seq_id _ihm_starting_model_seq_dif.comp_id _ihm_starting_model_seq_dif.starting_model_id _ihm_starting_model_seq_dif.db_entity_id _ihm_starting_model_seq_dif.db_asym_id _ihm_starting_model_seq_dif.db_seq_id _ihm_starting_model_seq_dif.db_comp_id _ihm_starting_model_seq_dif.details 1 1 A 1 MET Nup84-m1 1 A 1 MSE "Conversion of modified residue MSE to MET" 2 2 C 62 GLU Nup84-m1 1 A 61 PHE "Point change of PHE to GLU" # ...abbreviated... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_starting_model_seq_dif # save_ # save__ihm_starting_model_seq_dif.id _item_description.description " A unique identifier for the entry." # _item.name "_ihm_starting_model_seq_dif.id" _item.category_id ihm_starting_model_seq_dif _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_starting_model_seq_dif.entity_id _item_description.description ; A unique identifier for the distinct molecular entities. This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY category. ; # _item.name "_ihm_starting_model_seq_dif.entity_id" _item.category_id ihm_starting_model_seq_dif _item.mandatory_code yes # _item_type.code code # _item_sub_category.id mm_poly_res_label # _item_linked.child_name "_ihm_starting_model_seq_dif.entity_id" _item_linked.parent_name "_entity_poly_seq.entity_id" # save_ # save__ihm_starting_model_seq_dif.asym_id _item_description.description ; An asym/strand identifier for the entity molecule. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_starting_model_seq_dif.asym_id" _item.category_id ihm_starting_model_seq_dif _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_starting_model_seq_dif.asym_id" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_starting_model_seq_dif.seq_id _item_description.description ; The residue index. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_starting_model_seq_dif.seq_id" _item.category_id ihm_starting_model_seq_dif _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label # _item_linked.child_name "_ihm_starting_model_seq_dif.seq_id" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_starting_model_seq_dif.comp_id _item_description.description ; The component identifier for the residue. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_starting_model_seq_dif.comp_id" _item.category_id ihm_starting_model_seq_dif _item.mandatory_code yes # _item_type.code ucode # _item_sub_category.id mm_poly_res_label # _item_linked.child_name "_ihm_starting_model_seq_dif.comp_id" _item_linked.parent_name "_entity_poly_seq.mon_id" # save_ # save__ihm_starting_model_seq_dif.starting_model_id _item_description.description ; Unique identifier for the starting model record. This data item is a pointer to _ihm_starting_model_details.starting_model_id in the IHM_STARTING_MODEL_DETAILS category. ; # _item.name "_ihm_starting_model_seq_dif.starting_model_id" _item.category_id ihm_starting_model_seq_dif _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_starting_model_seq_dif.starting_model_id" _item_linked.parent_name "_ihm_starting_model_details.starting_model_id" # save_ # save__ihm_starting_model_seq_dif.db_entity_id _item_description.description " The molecular entity of the database starting model." # _item.name "_ihm_starting_model_seq_dif.db_entity_id" _item.category_id ihm_starting_model_seq_dif _item.mandatory_code no # _item_type.code code # save_ # save__ihm_starting_model_seq_dif.db_asym_id _item_description.description " The asym/strand identifier for the entity molecule of the database starting model." # _item.name "_ihm_starting_model_seq_dif.db_asym_id" _item.category_id ihm_starting_model_seq_dif _item.mandatory_code yes # _item_type.code code # save_ # save__ihm_starting_model_seq_dif.db_seq_id _item_description.description " The corresponding residue index of the database starting model." # _item.name "_ihm_starting_model_seq_dif.db_seq_id" _item.category_id ihm_starting_model_seq_dif _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_starting_model_seq_dif.db_comp_id _item_description.description " The correspinding component identifier for the residue in the database starting model." # _item.name "_ihm_starting_model_seq_dif.db_comp_id" _item.category_id ihm_starting_model_seq_dif _item.mandatory_code yes # _item_type.code ucode # save_ # save__ihm_starting_model_seq_dif.details _item_description.description ; A description of special aspects of the point differences between the sequence of the entity or biological unit described in the data block and that in the starting model referenced from a database. ; # _item.name "_ihm_starting_model_seq_dif.details" _item.category_id ihm_starting_model_seq_dif _item.mandatory_code no # _item_type.code text # loop_ _item_examples.case "Conversion of modified residue MSE to MET" "Point change of PHE to GLU" # save_ # save_ihm_model_representation _category.description ; Data items in the IHM_MODEL_REPRESENTATION category lists the various mono or multi-scale model representations used in the integrative modeling study. ; _category.id ihm_model_representation _category.mandatory_code no # _category_key.name "_ihm_model_representation.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_model_representation.id _ihm_model_representation.name _ihm_model_representation.details 1 'multi-scale representation of the complete nuclear pore complex' . 2 'atomic representation of selected subunits of the nuclear pore complex' . # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_model_representation # save_ # save__ihm_model_representation.id _item_description.description " A unique identifier for the model representation." # _item.name "_ihm_model_representation.id" _item.category_id ihm_model_representation _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_model_representation.name _item_description.description " Name/brief description for the model representation." # _item.name "_ihm_model_representation.name" _item.category_id ihm_model_representation _item.mandatory_code no # _item_type.code line # save_ # save__ihm_model_representation.details _item_description.description " Additional details about the model representation." # _item.name "_ihm_model_representation.details" _item.category_id ihm_model_representation _item.mandatory_code no # _item_type.code text # save_ # save_ihm_model_representation_details _category.description ; Data items in the IHM_MODEL_REPRESENTATION_DETAILS category records the details about the architecture and representation of structural models involved in the integrative modeling study. ; _category.id ihm_model_representation_details _category.mandatory_code no # _category_key.name "_ihm_model_representation_details.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_model_representation_details.id _ihm_model_representation_details.representation_id _ihm_model_representation_details.entity_poly_segment_id _ihm_model_representation_details.entity_id _ihm_model_representation_details.entity_description _ihm_model_representation_details.entity_asym_id _ihm_model_representation_details.model_object_primitive _ihm_model_representation_details.starting_model_id _ihm_model_representation_details.model_mode _ihm_model_representation_details.model_granularity _ihm_model_representation_details.model_object_count 1 1 1 1 Nup84 A sphere Nup84-m1 flexible by-feature 1 2 1 2 1 Nup84 A sphere Nup84-m1 rigid by-residue . 3 1 3 1 Nup84 A sphere Nup84-m1 flexible by-feature 1 4 1 4 1 Nup84 A sphere Nup84-m1 rigid by-residue . 5 1 5 1 Nup84 A sphere Nup84-m1 flexible by-feature 1 6 1 6 1 Nup84 A sphere Nup84-m1 rigid by-residue . 7 1 6 1 Nup84 A sphere Nup84-m1 flexible by-feature 3 8 1 7 1 Nup84 A sphere Nup84-m1 flexible by-feature 1 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_model_representation_details # save_ # save__ihm_model_representation_details.id _item_description.description " A unique identifier for the category." # _item.name "_ihm_model_representation_details.id" _item.category_id ihm_model_representation_details _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_model_representation_details.representation_id _item_description.description ; An identifier that collects or groups together a set of representations. This data item is a pointer to _ihm_model_representation.id in the IHM_MODEL_REPRESENTATION category. ; # _item.name "_ihm_model_representation_details.representation_id" _item.category_id ihm_model_representation_details _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_model_representation_details.representation_id" _item_linked.parent_name "_ihm_model_representation.id" # save_ # save__ihm_model_representation_details.entity_poly_segment_id _item_description.description ; The identifier for the polymeric segment in the representation. This data item is a pointer to _ihm_entity_poly_segment.id in the IHM_ENTITY_POLY_SEGMENT category. ; # _item.name "_ihm_model_representation_details.entity_poly_segment_id" _item.category_id ihm_model_representation_details _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_model_representation_details.entity_poly_segment_id" _item_linked.parent_name "_ihm_entity_poly_segment.id" # save_ # save__ihm_model_representation_details.entity_id _item_description.description ; A unique identifier distinct molecular entities. This data item is a pointer to _entity.id in the ENTITY category. ; # _item.name "_ihm_model_representation_details.entity_id" _item.category_id ihm_model_representation_details _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_model_representation_details.entity_id" _item_linked.parent_name "_entity.id" # save_ # save__ihm_model_representation_details.entity_description _item_description.description " A text description of the molecular entity" # _item.name "_ihm_model_representation_details.entity_description" _item.category_id ihm_model_representation_details _item.mandatory_code no # _item_type.code line # save_ # save__ihm_model_representation_details.entity_asym_id _item_description.description ; An asym/strand identifier for the entity molecule. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_model_representation_details.entity_asym_id" _item.category_id ihm_model_representation_details _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_model_representation_details.entity_asym_id" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_model_representation_details.model_object_primitive _item_description.description " The primitive object used to model this segment." # _item.name "_ihm_model_representation_details.model_object_primitive" _item.category_id ihm_model_representation_details _item.mandatory_code no # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail atomistic . sphere . gaussian . other . # save_ # save__ihm_model_representation_details.starting_model_id _item_description.description ; The identifier for the starting structural model. This data item is a pointer to _ihm_starting_model_details.starting_model_id in the IHM_STARTING_MODEL_DETAILS category. ; # _item.name "_ihm_model_representation_details.starting_model_id" _item.category_id ihm_model_representation_details _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_ihm_model_representation_details.starting_model_id" _item_linked.parent_name "_ihm_starting_model_details.starting_model_id" # save_ # save__ihm_model_representation_details.model_mode _item_description.description " The manner in which the segment is modeled." # _item.name "_ihm_model_representation_details.model_mode" _item.category_id ihm_model_representation_details _item.mandatory_code no # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail rigid . flexible . # save_ # save__ihm_model_representation_details.model_granularity _item_description.description " The level of detail at which model primitive objects are applied to the structure." # _item.name "_ihm_model_representation_details.model_granularity" _item.category_id ihm_model_representation_details _item.mandatory_code no # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail by-atom "atomistic coordinate representation" by-residue "coordinates represent the alpha carbon position of a residue" multi-residue "coordinates represent the center of mass of a set of residues" by-feature "coordinates represent center or trace along the feature" # save_ # save__ihm_model_representation_details.model_object_count _item_description.description " The number of primitive objects used to model a feature in the case of 'by-feature' granularity." # _item.name "_ihm_model_representation_details.model_object_count" _item.category_id ihm_model_representation_details _item.mandatory_code no # _item_type.code int # save_ # save__ihm_model_representation_details.description _item_description.description " Additional description regarding the model representation." # _item.name "_ihm_model_representation_details.description" _item.category_id ihm_model_representation_details _item.mandatory_code no # _item_type.code text # save_ # save_ihm_struct_assembly_details _category.description ; Data items in the IHM_STRUCT_ASSEMBLY_DETAILS category records the details of the structural assemblies and used in the integrative modeling. ; _category.id ihm_struct_assembly_details _category.mandatory_code no # _category_key.name "_ihm_struct_assembly_details.id" # loop_ _category_group.id inclusive_group ihm_group # loop_ _category_examples.detail _category_examples.case ; Example 1 - Non-hierarchical assemblies with self-parent ; ; loop_ _ihm_struct_assembly_details.id _ihm_struct_assembly_details.assembly_id _ihm_struct_assembly_details.parent_assembly_id _ihm_struct_assembly_details.entity_description _ihm_struct_assembly_details.entity_id _ihm_struct_assembly_details.asym_id _ihm_struct_assembly_details.entity_poly_segment_id 1 1 1 Nup84 1 A 1 2 1 1 Nup85 2 B 2 3 1 1 Nup120 3 C 3 4 2 2 Nup133 4 D 4 5 2 2 Nup145 5 E 5 6 3 3 Seh1 6 F 6 7 3 3 Sec13 7 G 7 #...abbreviated... ; ; Example 2 - Hierarchical assembly ; ; loop_ _ihm_struct_assembly_details.id _ihm_struct_assembly_details.assembly_id _ihm_struct_assembly_details.parent_assembly_id _ihm_struct_assembly_details.entity_description _ihm_struct_assembly_details.entity_id _ihm_struct_assembly_details.asym_id _ihm_struct_assembly_details.entity_poly_segment_id 1 0 0 Nup84 1 A 1 2 0 0 Nup85 2 B 2 3 0 0 Nup120 3 C 3 4 0 0 Nup133 4 D 4 5 0 0 Nup145 5 E 5 6 0 0 Seh1 6 F 6 7 0 0 Sec13 7 G 7 8 1 0 Nup84 1 A 1 9 1 0 Nup85 2 B 2 10 1 0 Nup145 5 E 5 11 1 0 Seh1 6 F 6 12 1 0 Sec13 7 G 7 13 2 1 Nup84 1 A 1 14 2 1 Nup85 2 B 2 #...abbreviated... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_struct_assembly_details # save_ # save__ihm_struct_assembly_details.id _item_description.description " A unique identifier for the structural assembly description." # _item.name "_ihm_struct_assembly_details.id" _item.category_id ihm_struct_assembly_details _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_struct_assembly_details.assembly_id _item_description.description ; An identifier for the structural assembly. This data item will remain the same for all components of an assembly. This data item is a pointer to _ihm_struct_assembly.id in the IHM_STRUCT_ASSEMBLY category. ; # _item.name "_ihm_struct_assembly_details.assembly_id" _item.category_id ihm_struct_assembly_details _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_struct_assembly_details.assembly_id" _item_linked.parent_name "_ihm_struct_assembly.id" # save_ # save__ihm_struct_assembly_details.parent_assembly_id _item_description.description ; The parent of this assembly in a hierarchy. This data item is a pointer to _ihm_struct_assembly.id in the IHM_STRUCT_ASSEMBLY category. This data item should point to the assembly id of the immediate parent in a hierarchy. By convention, the full assembly (top of hierarchy) is assigned parent id 0 (zero). In case of assemblies that do not conform to a hierarchy, _ihm_struct_assembly_details.parent_assembly_id is the same as _ihm_struct_assembly_details.assembly_id indicating a self-parent. ; # _item.name "_ihm_struct_assembly_details.parent_assembly_id" _item.category_id ihm_struct_assembly_details _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_struct_assembly_details.parent_assembly_id" _item_linked.parent_name "_ihm_struct_assembly.id" # save_ # save__ihm_struct_assembly_details.entity_description _item_description.description " A text description of the molecular entity" # _item.name "_ihm_struct_assembly_details.entity_description" _item.category_id ihm_struct_assembly_details _item.mandatory_code no # _item_type.code line # save_ # save__ihm_struct_assembly_details.entity_id _item_description.description ; A unique identifier for distinct molecular entities. This data item is a pointer to _entity.id in the ENTITY category. ; # _item.name "_ihm_struct_assembly_details.entity_id" _item.category_id ihm_struct_assembly_details _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_struct_assembly_details.entity_id" _item_linked.parent_name "_entity.id" # save_ # save__ihm_struct_assembly_details.asym_id _item_description.description ; An asym/strand identifier for the component in the assembly. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_struct_assembly_details.asym_id" _item.category_id ihm_struct_assembly_details _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_struct_assembly_details.asym_id" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_struct_assembly_details.entity_poly_segment_id _item_description.description ; The identifier for the polymeric segment in the assembly. This data item is a pointer to _ihm_entity_poly_segment.id in the IHM_ENTITY_POLY_SEGMENT category. ; # _item.name "_ihm_struct_assembly_details.entity_poly_segment_id" _item.category_id ihm_struct_assembly_details _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_struct_assembly_details.entity_poly_segment_id" _item_linked.parent_name "_ihm_entity_poly_segment.id" # save_ # save_ihm_struct_assembly _category.description ; Data items in the IHM_STRUCT_ASSEMBLY category lists all the structural assemblies used in the integrative modeling study. ; _category.id ihm_struct_assembly _category.mandatory_code no # _category_key.name "_ihm_struct_assembly.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_struct_assembly.id _ihm_struct_assembly.name _ihm_struct_assembly.description 1 "Nup84 sub-complex" "Subunits in the Nup84 sub-complex" 2 "Nup82 sub-complex" "Subunits in the Nup82 sub-complex" # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_struct_assembly # save_ # save__ihm_struct_assembly.id _item_description.description " A unique identifier for the structural assembly." # _item.name "_ihm_struct_assembly.id" _item.category_id ihm_struct_assembly _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_struct_assembly.name _item_description.description " A name for the structural assembly." # _item.name "_ihm_struct_assembly.name" _item.category_id ihm_struct_assembly _item.mandatory_code no # _item_type.code line # save_ # save__ihm_struct_assembly.description _item_description.description " Description of the structural assembly." # _item.name "_ihm_struct_assembly.description" _item.category_id ihm_struct_assembly _item.mandatory_code no # _item_type.code text # save_ # save_ihm_struct_assembly_class _category.description ; Data items in the IHM_STRUCT_ASSEMBLY_CLASS category lists all the structural assembly classes relevant to the entry. This category provides a mechanism to define classes of the structural assemblies. ; _category.id ihm_struct_assembly_class _category.mandatory_code no # _category_key.name "_ihm_struct_assembly_class.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_struct_assembly_class.id _ihm_struct_assembly_class.name _ihm_struct_assembly_class.type _ihm_struct_assembly_class.description 1 "TAD" "Structural Hierarchy" . 2 "CHROMATIN" "Structural Hierarchy" . # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_struct_assembly_class # save_ # save__ihm_struct_assembly_class.id _item_description.description " A unique identifier for the structural assembly class." # _item.name "_ihm_struct_assembly_class.id" _item.category_id ihm_struct_assembly_class _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_struct_assembly_class.name _item_description.description " A user provided name for the class." # _item.name "_ihm_struct_assembly_class.name" _item.category_id ihm_struct_assembly_class _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code line # loop_ _item_examples.case TAD Chromatin # save_ # save__ihm_struct_assembly_class.type _item_description.description " The type of classifier." # _item.name "_ihm_struct_assembly_class.type" _item.category_id ihm_struct_assembly_class _item.mandatory_code no # _item_type.code line # loop_ _item_enumeration.value "Structural Hierarchy" Functional Other # save_ # save__ihm_struct_assembly_class.description _item_description.description " Additional description regarding the class." # _item.name "_ihm_struct_assembly_class.description" _item.category_id ihm_struct_assembly_class _item.mandatory_code no # _item_type.code text # save_ # save_ihm_struct_assembly_class_link _category.description ; Data items in the IHM_STRUCT_ASSEMBLY_CLASS_LINK category provides details regarding the structural assembly classes. This category provides a mechanism to identify the classes to which structural assemblies belong. ; _category.id ihm_struct_assembly_class_link _category.mandatory_code no # loop_ _category_key.name "_ihm_struct_assembly_class_link.class_id" "_ihm_struct_assembly_class_link.assembly_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_struct_assembly_class_link.class_id _ihm_struct_assembly_class_link.assembly_id 1 1 1 2 1 3 2 4 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_struct_assembly_class_link # save_ # save__ihm_struct_assembly_class_link.class_id _item_description.description ; An identifier for the structural assembly class. This data item is a pointer to _ihm_struct_assembly_class.id in the IHM_STRUCT_ASSEMBLY_CLASS category. ; # _item.name "_ihm_struct_assembly_class_link.class_id" _item.category_id ihm_struct_assembly_class_link _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_struct_assembly_class_link.class_id" _item_linked.parent_name "_ihm_struct_assembly_class.id" # save_ # save__ihm_struct_assembly_class_link.assembly_id _item_description.description ; An identifier for the structural assembly. This data item is a pointer to _ihm_struct_assembly.id in the IHM_STRUCT_ASSEMBLY category. ; # _item.name "_ihm_struct_assembly_class_link.assembly_id" _item.category_id ihm_struct_assembly_class_link _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_struct_assembly_class_link.assembly_id" _item_linked.parent_name "_ihm_struct_assembly.id" # save_ # save_ihm_modeling_protocol _category.description ; Data items in the IHM_MODELING_PROTOCOL category lists all modeling protocols used in the integrative modeling study. ; _category.id ihm_modeling_protocol _category.mandatory_code no # _category_key.name "_ihm_modeling_protocol.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; _ihm_modeling_protocol.id _ihm_modeling_protocol.num_steps _ihm_modeling_protocol.protocol_name _ihm_modeling_protocol.details 1 2 'Multi-scale modeling of the Nup84 sub-complex' ? 2 3 'Multi-scale modeling of the Nuclear pore complex' ? ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_modeling_protocol # save_ # save__ihm_modeling_protocol.id _item_description.description " A unique identifier for the modeling protocol." # _item.name "_ihm_modeling_protocol.id" _item.category_id ihm_modeling_protocol _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_modeling_protocol.num_steps _item_description.description " Number of independent steps in the modeling protocol." # _item.name "_ihm_modeling_protocol.num_steps" _item.category_id ihm_modeling_protocol _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_modeling_protocol.protocol_name _item_description.description " The name for the modeling protocol." # _item.name "_ihm_modeling_protocol.protocol_name" _item.category_id ihm_modeling_protocol _item.mandatory_code no # _item_type.code line # loop_ _item_examples.case "Multi-scale modeling of the Nuclear Pore Complex" "Multi-state modeling of the RNA 4-Way Junction" # save_ # save__ihm_modeling_protocol.details _item_description.description " Additional details about the modeling protocol." # _item.name "_ihm_modeling_protocol.details" _item.category_id ihm_modeling_protocol _item.mandatory_code no # _item_type.code text # save_ # save_ihm_modeling_protocol_details _category.description ; Data items in the IHM_MODELING_PROTOCOL_DETAILS category records the step-wise details of the integrative modeling workflow. ; _category.id ihm_modeling_protocol_details _category.mandatory_code no # _category_key.name "_ihm_modeling_protocol_details.id" # loop_ _category_group.id inclusive_group ihm_group # loop_ _category_examples.detail _category_examples.case ; Example 1 - ; ; _ihm_modeling_protocol_details.id _ihm_modeling_protocol_details.protocol_id _ihm_modeling_protocol_details.step_id _ihm_modeling_protocol_details.struct_assembly_id _ihm_modeling_protocol_details.dataset_group_id _ihm_modeling_protocol_details.struct_assembly_description _ihm_modeling_protocol_details.step_name _ihm_modeling_protocol_details.step_method _ihm_modeling_protocol_details.num_models_begin _ihm_modeling_protocol_details.num_models_end _ihm_modeling_protocol_details.multi_scale_flag _ihm_modeling_protocol_details.multi_state_flag _ihm_modeling_protocol_details.ordered_flag _ihm_modeling_protocol_details.ensemble_flag 1 1 1 1 1 'Nup84 sub-complex' 'Sampling' 'Replica exchange monte carlo' 0 7500 YES NO NO YES 2 1 2 1 2 'Nup84 sub-complex' 'Sampling' 'Replica exchange monte carlo' 7500 15000 YES NO NO YES ; ; Example 2 - ; ; _ihm_modeling_protocol_details.id _ihm_modeling_protocol_details.protocol_id _ihm_modeling_protocol_details.step_id _ihm_modeling_protocol_details.struct_assembly_id _ihm_modeling_protocol_details.dataset_group_id _ihm_modeling_protocol_details.struct_assembly_description _ihm_modeling_protocol_details.step_name _ihm_modeling_protocol_details.step_method _ihm_modeling_protocol_details.num_models_begin _ihm_modeling_protocol_details.num_models_end _ihm_modeling_protocol_details.multi_scale_flag _ihm_modeling_protocol_details.multi_state_flag _ihm_modeling_protocol_details.ordered_flag _ihm_modeling_protocol_details.ensemble_flag 1 1 1 1 1 'PhoQ' 'Sampling' 'Monte carlo' 0 5000 YES YES NO YES 2 1 1 2 1 'PhoQ' 'Sampling' 'Monte carlo' 0 5000 YES YES NO YES ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_modeling_protocol_details # save_ # save__ihm_modeling_protocol_details.id _item_description.description " A unique identifier for the modeling protocol/step combination." # _item.name "_ihm_modeling_protocol_details.id" _item.category_id ihm_modeling_protocol_details _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_modeling_protocol_details.protocol_id _item_description.description ; An index for the modeling protocol carried out. This data item is a pointer to _ihm_modeling_protocol.id in the IHM_MODELING_PROTOCOL category. ; # _item.name "_ihm_modeling_protocol_details.protocol_id" _item.category_id ihm_modeling_protocol_details _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_modeling_protocol_details.protocol_id" _item_linked.parent_name "_ihm_modeling_protocol.id" # save_ # save__ihm_modeling_protocol_details.step_id _item_description.description " An index for a particular step within the modeling protocol." # _item.name "_ihm_modeling_protocol_details.step_id" _item.category_id ihm_modeling_protocol_details _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_modeling_protocol_details.struct_assembly_id _item_description.description ; An index for the structural assembly being modeled. This is an indicator to whether the whole assembly is modeled or if only a subset of the structural assembly is modeled. This data item is a pointer to _ihm_struct_assembly.id in the IHM_STRUCT_ASSEMBLY category. The IHM_STRUCT_ASSEMBLY category provides the details regarding the different structural assemblies used in the modeling. The default value for this data item is "1", indicating that the entire assembly is being modeled. ; # _item.name "_ihm_modeling_protocol_details.struct_assembly_id" _item.category_id ihm_modeling_protocol_details _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_modeling_protocol_details.struct_assembly_id" _item_linked.parent_name "_ihm_struct_assembly.id" # _item_default.value 1 # save_ # save__ihm_modeling_protocol_details.dataset_group_id _item_description.description ; An index for the dataset group being used in the modeling protocol. This data item is a pointer to the _ihm_dataset_group.id in the IHM_DATASET_GROUP category. ; # _item.name "_ihm_modeling_protocol_details.dataset_group_id" _item.category_id ihm_modeling_protocol_details _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_modeling_protocol_details.dataset_group_id" _item_linked.parent_name "_ihm_dataset_group.id" # save_ # save__ihm_modeling_protocol_details.struct_assembly_description _item_description.description " A textual description of the structural assembly being modeled." # _item.name "_ihm_modeling_protocol_details.struct_assembly_description" _item.category_id ihm_modeling_protocol_details _item.mandatory_code no # _item_type.code line # loop_ _item_examples.case "Nup84 sub-complex" PhoQ # save_ # save__ihm_modeling_protocol_details.step_name _item_description.description " The name or type of the modeling step." # _item.name "_ihm_modeling_protocol_details.step_name" _item.category_id ihm_modeling_protocol_details _item.mandatory_code no # _item_type.code line # loop_ _item_examples.case Sampling/Scoring Refinement # save_ # save__ihm_modeling_protocol_details.step_method _item_description.description " Description of the method involved in the modeling step." # _item.name "_ihm_modeling_protocol_details.step_method" _item.category_id ihm_modeling_protocol_details _item.mandatory_code no # _item_type.code line # loop_ _item_examples.case "Replica exchange monte carlo" "Simulated annealing monte carlo" "Monte carlo sampling" # save_ # save__ihm_modeling_protocol_details.num_models_begin _item_description.description " The number of models in the beginning of the step." # _item.name "_ihm_modeling_protocol_details.num_models_begin" _item.category_id ihm_modeling_protocol_details _item.mandatory_code no # _item_type.code int # save_ # save__ihm_modeling_protocol_details.num_models_end _item_description.description " The number of models at the end of the step." # _item.name "_ihm_modeling_protocol_details.num_models_end" _item.category_id ihm_modeling_protocol_details _item.mandatory_code no # _item_type.code int # save_ # save__ihm_modeling_protocol_details.multi_scale_flag _item_description.description " A flag to indicate if the modeling is multi scale." # _item.name "_ihm_modeling_protocol_details.multi_scale_flag" _item.category_id ihm_modeling_protocol_details _item.mandatory_code no # _item_type.code ucode # loop_ _item_enumeration.value _item_enumeration.detail YES . NO . # save_ # save__ihm_modeling_protocol_details.multi_state_flag _item_description.description " A flag to indicate if the modeling is multi state." # _item.name "_ihm_modeling_protocol_details.multi_state_flag" _item.category_id ihm_modeling_protocol_details _item.mandatory_code no # _item_type.code ucode # loop_ _item_enumeration.value _item_enumeration.detail YES . NO . # save_ # save__ihm_modeling_protocol_details.ordered_flag _item_description.description " A flag to indicate if the modeling involves an ensemble ordered by time or other order." # _item.name "_ihm_modeling_protocol_details.ordered_flag" _item.category_id ihm_modeling_protocol_details _item.mandatory_code no # _item_type.code ucode # loop_ _item_enumeration.value _item_enumeration.detail YES . NO . # save_ # save__ihm_modeling_protocol_details.ensemble_flag _item_description.description " A flag to indicate if the modeling involves an ensemble." # _item.name "_ihm_modeling_protocol_details.ensemble_flag" _item.category_id ihm_modeling_protocol_details _item.mandatory_code no # _item_type.code ucode # loop_ _item_enumeration.value _item_enumeration.detail YES . NO . # save_ # save__ihm_modeling_protocol_details.script_file_id _item_description.description ; The file id corresponding to the script used in the modeling protocol step. This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES category. ; # _item.name "_ihm_modeling_protocol_details.script_file_id" _item.category_id ihm_modeling_protocol_details _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_modeling_protocol_details.script_file_id" _item_linked.parent_name "_ihm_external_files.id" # save_ # save__ihm_modeling_protocol_details.software_id _item_description.description ; Identifier to the software used in the modeling protocol step. This data item is a pointer to the _software.pdbx_ordinal in the SOFTWARE category. ; # _item.name "_ihm_modeling_protocol_details.software_id" _item.category_id ihm_modeling_protocol_details _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_modeling_protocol_details.software_id" _item_linked.parent_name "_software.pdbx_ordinal" # save_ # save__ihm_modeling_protocol_details.description _item_description.description " Textual description of the protocol step." # _item.name "_ihm_modeling_protocol_details.description" _item.category_id ihm_modeling_protocol_details _item.mandatory_code no # _item_type.code text # save_ # save_ihm_multi_state_modeling _category.description ; Data items in the IHM_MULTI_STATE_MODELING category records the details of the multi-state modeling protocol, if applicable. ; _category.id ihm_multi_state_modeling _category.mandatory_code no # _category_key.name "_ihm_multi_state_modeling.state_id" # loop_ _category_group.id inclusive_group ihm_group # loop_ _category_examples.detail _category_examples.case ; Example 1 - conformational change ; ; loop_ _ihm_multi_state_modeling.state_id _ihm_multi_state_modeling.state_group_id _ihm_multi_state_modeling.population_fraction _ihm_multi_state_modeling.state_type _ihm_multi_state_modeling.state_name _ihm_multi_state_modeling.experiment_type _ihm_multi_state_modeling.details 1 1 0.5 'conformational change' 'open' 'Fraction of bulk' 'open state ensemble 1' 2 1 0.5 'conformational change' 'closed' 'Fraction of bulk' 'closed state ensemble 2' ; ; Example 2 - ligand binding ; ; loop_ _ihm_multi_state_modeling.state_id _ihm_multi_state_modeling.state_group_id _ihm_multi_state_modeling.population_fraction _ihm_multi_state_modeling.state_type _ihm_multi_state_modeling.state_name _ihm_multi_state_modeling.experiment_type _ihm_multi_state_modeling.details 1 1 0.25 'ligand binding' 'unbound' 'Fraction of bulk' 'unbound' 2 1 0.75 'ligand binding' 'bound' 'Fraction of bulk' 'bound to heme' ; ; Example 3 - complex formation ; ; loop_ _ihm_multi_state_modeling.state_id _ihm_multi_state_modeling.state_group_id _ihm_multi_state_modeling.population_fraction _ihm_multi_state_modeling.state_type _ihm_multi_state_modeling.state_name _ihm_multi_state_modeling.experiment_type _ihm_multi_state_modeling.details 1 1 . 'complex formation' 'unbound' 'Fraction of bulk' 'unbound molecule 1' 2 1 . 'complex formation' 'unbound' 'Fraction of bulk' 'unbound molecule 2' 3 1 . 'complex formation' 'bound' 'Fraction of bulk' 'bound molecules 1 and 2' ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_multi_state_modeling # save_ # save__ihm_multi_state_modeling.state_id _item_description.description " A unique identifier for a particular state in the multi-state modeling." # _item.name "_ihm_multi_state_modeling.state_id" _item.category_id ihm_multi_state_modeling _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_multi_state_modeling.state_group_id _item_description.description ; An identifier for a collections of states in the multi-state modeling. This data item can be used when structural models belong to diffent multi-state modeling types. ; # _item.name "_ihm_multi_state_modeling.state_group_id" _item.category_id ihm_multi_state_modeling _item.mandatory_code no # _item_type.code int # save_ # save__ihm_multi_state_modeling.population_fraction _item_description.description " A fraction representing the population of the particular state." # _item.name "_ihm_multi_state_modeling.population_fraction" _item.category_id ihm_multi_state_modeling _item.mandatory_code no # _item_type.code float # save_ # save__ihm_multi_state_modeling.population_fraction_sd _item_description.description " The standard deviation of the population fraction." # _item.name "_ihm_multi_state_modeling.population_fraction_sd" _item.category_id ihm_multi_state_modeling _item.mandatory_code no # _item_type.code float # save_ # save__ihm_multi_state_modeling.state_type _item_description.description " The type that the multiple states being modeled belong to." # _item.name "_ihm_multi_state_modeling.state_type" _item.category_id ihm_multi_state_modeling _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code line # loop_ _item_examples.case "conformational change" "ligand binding" "complex formation" "complex dissociation" # save_ # save__ihm_multi_state_modeling.state_name _item_description.description " A descriptive name for the state." # _item.name "_ihm_multi_state_modeling.state_name" _item.category_id ihm_multi_state_modeling _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code line # loop_ _item_examples.case open closed bound unbound active inactive relaxed tensed # save_ # save__ihm_multi_state_modeling.experiment_type _item_description.description " The type of multi-state modeling experiment carried out." # _item.name "_ihm_multi_state_modeling.experiment_type" _item.category_id ihm_multi_state_modeling _item.mandatory_code no # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail "Fraction of bulk" "Multiple states from a bulk sample, where a fraction of molecules are in one state and another fraction are in a different state" "Single molecule" "A single molecule experiment, where the different states are adopted by the same molecule at different points in time and the experiment provides a convolution of these states" # save_ # save__ihm_multi_state_modeling.details _item_description.description " Additional textual details of the multi-state modeling, if required." # _item.name "_ihm_multi_state_modeling.details" _item.category_id ihm_multi_state_modeling _item.mandatory_code no # _item_type.code text # loop_ _item_examples.case "open state ensemble 1" "closed state ensemble 2" "bound to heme" # save_ # save_ihm_multi_state_model_group_link _category.description ; IHM_MULTI_STATE_MODEL_GROUP_LINK category provides the list of models groups corresponding to a particular state. ; _category.id ihm_multi_state_model_group_link _category.mandatory_code no # _category_key.name "_ihm_multi_state_model_group_link.model_group_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_multi_state_model_group_link.state_id _ihm_multi_state_model_group_link.model_group_id 1 1 1 2 1 3 1 4 1 5 ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_multi_state_model_group_link # save_ # save__ihm_multi_state_model_group_link.state_id _item_description.description ; An identifier for the state. This data item is a pointer to _ihm_multi_state_modeling.state_id in the IHM_MULTI_STATE_MODELING category. ; # _item.name "_ihm_multi_state_model_group_link.state_id" _item.category_id ihm_multi_state_model_group_link _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_multi_state_model_group_link.state_id" _item_linked.parent_name "_ihm_multi_state_modeling.state_id" # save_ # save__ihm_multi_state_model_group_link.model_group_id _item_description.description ; An identifier for the structural model group. This data item is a pointer to _ihm_model_group.id in the IHM_MODEL_GROUP category. ; # _item.name "_ihm_multi_state_model_group_link.model_group_id" _item.category_id ihm_multi_state_model_group_link _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_multi_state_model_group_link.model_group_id" _item_linked.parent_name "_ihm_model_group.id" # save_ # save_ihm_ordered_ensemble _category.description ; Data items in the IHM_ORDERED_ENSEMBLE category records the details of the ensembles ordered by time or other order. Ordered ensembles are described as directed graphs with edges between nodes representing models or model groups. ; _category.id ihm_ordered_ensemble _category.mandatory_code no # loop_ _category_key.name "_ihm_ordered_ensemble.edge_id" "_ihm_ordered_ensemble.process_id" # loop_ _category_group.id inclusive_group ihm_group # loop_ _category_examples.detail _category_examples.case ; Example 1 - Linear process ; ; loop_ _ihm_ordered_ensemble.process_id _ihm_ordered_ensemble.process_description _ihm_ordered_ensemble.edge_id _ihm_ordered_ensemble.edge_description _ihm_ordered_ensemble.step_id _ihm_ordered_ensemble.step_description _ihm_ordered_ensemble.ordered_by _ihm_ordered_ensemble.model_group_id_begin _ihm_ordered_ensemble.model_group_id_end 1 . 1 . 1 . 'time steps' 1 2 1 . 2 . 2 . 'time steps' 2 3 1 . 3 . 3 . 'time steps' 3 4 1 . 4 . 4 . 'time steps' 4 5 # ... abbreviated ... ; ; Example 2 - Cyclic process ; ; loop_ _ihm_ordered_ensemble.process_id _ihm_ordered_ensemble.edge_id _ihm_ordered_ensemble.step_id _ihm_ordered_ensemble.ordered_by _ihm_ordered_ensemble.model_group_id_begin _ihm_ordered_ensemble.model_group_id_end 1 1 1 'time steps' 1 2 1 2 2 'time steps' 2 3 1 3 3 'time steps' 3 4 1 4 4 'time steps' 4 1 # ... abbreviated ... ; ; Example 3 - Branched process ; ; loop_ _ihm_ordered_ensemble.process_id _ihm_ordered_ensemble.edge_id _ihm_ordered_ensemble.step_id _ihm_ordered_ensemble.ordered_by _ihm_ordered_ensemble.model_group_id_begin _ihm_ordered_ensemble.model_group_id_end 1 1 1 'time steps' 1 2 1 2 2 'time steps' 2 3 1 3 2 'time steps' 2 4 1 4 3 'time steps' 3 5 1 5 3 'time steps' 4 6 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_ordered_ensemble # save_ # save__ihm_ordered_ensemble.process_id _item_description.description ; An identifier for the ordered process. Forms the category key together with _ihm_ordered_ensemble.edge_id. ; # _item.name "_ihm_ordered_ensemble.process_id" _item.category_id ihm_ordered_ensemble _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_ordered_ensemble.process_description _item_description.description " Description of the ordered process." # _item.name "_ihm_ordered_ensemble.process_description" _item.category_id ihm_ordered_ensemble _item.mandatory_code no # _item_type.code text # save_ # save__ihm_ordered_ensemble.edge_id _item_description.description ; An identifier that describes an edge in a directed graph, which represents an ordered ensemble. Forms the category key together with _ihm_ordered_ensemble.process_id. ; # _item.name "_ihm_ordered_ensemble.edge_id" _item.category_id ihm_ordered_ensemble _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_ordered_ensemble.edge_description _item_description.description " Description of the edge." # _item.name "_ihm_ordered_ensemble.edge_description" _item.category_id ihm_ordered_ensemble _item.mandatory_code no # _item_type.code text # save_ # save__ihm_ordered_ensemble.step_id _item_description.description " Identifier for a particular step in the ordered process." # _item.name "_ihm_ordered_ensemble.step_id" _item.category_id ihm_ordered_ensemble _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_ordered_ensemble.step_description _item_description.description " Description of the step." # _item.name "_ihm_ordered_ensemble.step_description" _item.category_id ihm_ordered_ensemble _item.mandatory_code no # _item_type.code text # save_ # save__ihm_ordered_ensemble.ordered_by _item_description.description " The parameter based on which the ordering is carried out." # _item.name "_ihm_ordered_ensemble.ordered_by" _item.category_id ihm_ordered_ensemble _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code line # loop_ _item_examples.case "time steps" "steps in an assembly process" "steps in a metabolic pathway" "steps in an interaction pathway" # save_ # save__ihm_ordered_ensemble.model_group_id_begin _item_description.description ; The model group id corresponding to the node at the origin of directed edge. This data item is a pointer to _ihm_model_group.id in the IHM_MODEL_GROUP category. ; # _item.name "_ihm_ordered_ensemble.model_group_id_begin" _item.category_id ihm_ordered_ensemble _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_ordered_ensemble.model_group_id_begin" _item_linked.parent_name "_ihm_model_group.id" # save_ # save__ihm_ordered_ensemble.model_group_id_end _item_description.description ; The model group id corresponding to the node at the end of the directed edge. This data item is a pointer to _ihm_model_group.id in the IHM_MODEL_GROUP category. ; # _item.name "_ihm_ordered_ensemble.model_group_id_end" _item.category_id ihm_ordered_ensemble _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_ordered_ensemble.model_group_id_end" _item_linked.parent_name "_ihm_model_group.id" # save_ # save_ihm_modeling_post_process _category.description ; Data items in the IHM_MODELING_POST_PROCESS category records the details of the post processing of the models/results of the modeling protocol. ; _category.id ihm_modeling_post_process _category.mandatory_code no # _category_key.name "_ihm_modeling_post_process.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_modeling_post_process.id _ihm_modeling_post_process.protocol_id _ihm_modeling_post_process.analysis_id _ihm_modeling_post_process.step_id _ihm_modeling_post_process.type _ihm_modeling_post_process.feature _ihm_modeling_post_process.num_models_begin _ihm_modeling_post_process.num_models_end 1 1 1 1 'filter' 'energy/score' 15000 6520 2 1 1 2 'cluster' 'dRMSD' 6520 6520 3 1 2 1 'filter' 'energy/score' 15000 6520 4 1 2 2 'filter' 'composition' 6520 6520 5 1 2 3 'cluster' 'dRMSD' 6520 6520 ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_modeling_post_process # save_ # save__ihm_modeling_post_process.id _item_description.description " A unique identifier for the post modeling analysis/step combination." # _item.name "_ihm_modeling_post_process.id" _item.category_id ihm_modeling_post_process _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_modeling_post_process.protocol_id _item_description.description ; An identifier for the modeling protocol, whose post modeling analysis is being carried out. This data item is a pointer to the _ihm_modeling_protocol.id in the IHM_MODELING_PROTOCOL category. ; # _item.name "_ihm_modeling_post_process.protocol_id" _item.category_id ihm_modeling_post_process _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_modeling_post_process.protocol_id" _item_linked.parent_name "_ihm_modeling_protocol.id" # save_ # save__ihm_modeling_post_process.analysis_id _item_description.description ; An identifier for the post modeling analysis. This data item accounts for multiple post-modeling analyses that can be carried out. ; # _item.name "_ihm_modeling_post_process.analysis_id" _item.category_id ihm_modeling_post_process _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_modeling_post_process.step_id _item_description.description ; In a multi-step process, this identifier denotes the particular step in the post modeling analysis. ; # _item.name "_ihm_modeling_post_process.step_id" _item.category_id ihm_modeling_post_process _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_modeling_post_process.struct_assembly_id _item_description.description ; An index for the structural assembly being processed. This is an indicator to whether the whole assembly is processed or if only a subset of the structural assembly is processed. This data item is a pointer to _ihm_struct_assembly.id in the IHM_STRUCT_ASSEMBLY category. ; # _item.name "_ihm_modeling_post_process.struct_assembly_id" _item.category_id ihm_modeling_post_process _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_modeling_post_process.struct_assembly_id" _item_linked.parent_name "_ihm_struct_assembly.id" # save_ # save__ihm_modeling_post_process.dataset_group_id _item_description.description ; An index for the dataset group being used in the post modeling process. This data item is a pointer to the _ihm_dataset_group.id in the IHM_DATASET_GROUP category. ; # _item.name "_ihm_modeling_post_process.dataset_group_id" _item.category_id ihm_modeling_post_process _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_modeling_post_process.dataset_group_id" _item_linked.parent_name "_ihm_dataset_group.id" # save_ # save__ihm_modeling_post_process.type _item_description.description " The type of post modeling analysis being carried out." # _item.name "_ihm_modeling_post_process.type" _item.category_id ihm_modeling_post_process _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail filter "post processing step involves filtering of models" cluster "post processing step involves clustering of models" rescore "post processing step involves rescoring of the models" validation "post processing step involves validation of the models" other "post processing step involves a different kind of analysis" none "no post processing is carried out" # save_ # save__ihm_modeling_post_process.feature _item_description.description " The parameter/feature used in the post modeling analysis." # _item.name "_ihm_modeling_post_process.feature" _item.category_id ihm_modeling_post_process _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail energy/score . RMSD . dRMSD . other . none . # save_ # save__ihm_modeling_post_process.feature_name _item_description.description " The name of the parameter/feature used in the post modeling analysis." # _item.name "_ihm_modeling_post_process.feature_name" _item.category_id ihm_modeling_post_process _item.mandatory_code no # _item_type.code line # loop_ _item_examples.case "Rosetta energy" "GOAP (orientation-dependent all-atom statistical potential)" # save_ # save__ihm_modeling_post_process.num_models_begin _item_description.description " The number of models at the beginning of the post processing step." # _item.name "_ihm_modeling_post_process.num_models_begin" _item.category_id ihm_modeling_post_process _item.mandatory_code no # _item_type.code int # save_ # save__ihm_modeling_post_process.num_models_end _item_description.description " The number of models the the end of the post processing step." # _item.name "_ihm_modeling_post_process.num_models_end" _item.category_id ihm_modeling_post_process _item.mandatory_code no # _item_type.code int # save_ # save__ihm_modeling_post_process.script_file_id _item_description.description ; The file id corresponding to the script used in the post processing step. This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES category. ; # _item.name "_ihm_modeling_post_process.script_file_id" _item.category_id ihm_modeling_post_process _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_modeling_post_process.script_file_id" _item_linked.parent_name "_ihm_external_files.id" # save_ # save__ihm_modeling_post_process.software_id _item_description.description ; Identifier to the software used in the post processing step. This data item is a pointer to the _software.pdbx_ordinal in the SOFTWARE category. ; # _item.name "_ihm_modeling_post_process.software_id" _item.category_id ihm_modeling_post_process _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_modeling_post_process.software_id" _item_linked.parent_name "_software.pdbx_ordinal" # save_ # save__ihm_modeling_post_process.details _item_description.description " Additional details regarding post processing." # _item.name "_ihm_modeling_post_process.details" _item.category_id ihm_modeling_post_process _item.mandatory_code no # _item_type.code text # save_ # save_ihm_ensemble_info _category.description ; Data items in the IHM_ENSEMBLE_INFO category records the details of the model clusters or ensembles obtained after sampling. ; _category.id ihm_ensemble_info _category.mandatory_code no # _category_key.name "_ihm_ensemble_info.ensemble_id" # loop_ _category_group.id inclusive_group ihm_group # loop_ _category_examples.detail _category_examples.case ; Example 1 - ; ; loop_ _ihm_ensemble_info.ensemble_id _ihm_ensemble_info.ensemble_name _ihm_ensemble_info.post_process_id _ihm_ensemble_info.model_group_id _ihm_ensemble_info.ensemble_clustering_method _ihm_ensemble_info.ensemble_clustering_feature _ihm_ensemble_info.num_ensemble_models _ihm_ensemble_info.num_ensemble_models_deposited _ihm_ensemble_info.ensemble_precision_value _ihm_ensemble_info.ensemble_file_id 1 'ensemble1' 2 1 Hierarchical dRMSD 2885 5 17.3 20 2 'ensemble2' 2 2 Hierarchical dRMSD 1401 5 19.2 21 3 'ensemble3' 5 . Hierarchical dRMSD 577 0 14.8 22 4 'ensemble4' 5 . Hierarchical dRMSD 404 0 10.8 23 ; ; Example 2 - ; ; loop_ _ihm_ensemble_info.ensemble_id _ihm_ensemble_info.ensemble_name _ihm_ensemble_info.post_process_id _ihm_ensemble_info.model_group_id _ihm_ensemble_info.ensemble_clustering_method _ihm_ensemble_info.ensemble_clustering_feature _ihm_ensemble_info.num_ensemble_models _ihm_ensemble_info.num_ensemble_models_deposited _ihm_ensemble_info.ensemble_precision_value _ihm_ensemble_info.ensemble_file_id 1 'open state' . 1 Hierarchical RMSD 2885 5 12.3 20 2 'closed state' . 2 Hierarchical RMSD 577 5 11.8 21 ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_ensemble_info # save_ # save__ihm_ensemble_info.ensemble_id _item_description.description " A unique id for the ensemble." # _item.name "_ihm_ensemble_info.ensemble_id" _item.category_id ihm_ensemble_info _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_ensemble_info.ensemble_name _item_description.description " An optional name for the cluster or ensemble for better description." # _item.name "_ihm_ensemble_info.ensemble_name" _item.category_id ihm_ensemble_info _item.mandatory_code no # _item_type.code line # loop_ _item_examples.case ensemble1 ensemble2 cluster1 cluster2 "open state" "closed state" # save_ # save__ihm_ensemble_info.post_process_id _item_description.description ; An identifier for the post modeling analyses carried out. This data item is a pointer to _ihm_modeling_post_process.id in the IHM_MODELING_POST_PROCESS category. ; # _item.name "_ihm_ensemble_info.post_process_id" _item.category_id ihm_ensemble_info _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_ensemble_info.post_process_id" _item_linked.parent_name "_ihm_modeling_post_process.id" # save_ # save__ihm_ensemble_info.model_group_id _item_description.description ; An identifier for the cluster or group of models being deposited. This data item is a pointer to the _ihm_model_group.id in the IHM_MODEL_GROUP category. ; # _item.name "_ihm_ensemble_info.model_group_id" _item.category_id ihm_ensemble_info _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_ensemble_info.model_group_id" _item_linked.parent_name "_ihm_model_group.id" # save_ # save__ihm_ensemble_info.model_group_superimposed_flag _item_description.description " Flag to identify if the models in a group or cluster are structurally aligned." # _item.name "_ihm_ensemble_info.model_group_superimposed_flag" _item.category_id ihm_ensemble_info _item.mandatory_code no # _item_type.code ucode # loop_ _item_enumeration.value YES NO # save_ # save__ihm_ensemble_info.ensemble_clustering_method _item_description.description " The clustering method used to obtain the ensemble, if applicable." # _item.name "_ihm_ensemble_info.ensemble_clustering_method" _item.category_id ihm_ensemble_info _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value Hierarchical "Partitioning (k-means)" "Density based threshold-clustering" Other # save_ # save__ihm_ensemble_info.ensemble_clustering_feature _item_description.description " The parameter/feature used for clustering the models, if applicable." # _item.name "_ihm_ensemble_info.ensemble_clustering_feature" _item.category_id ihm_ensemble_info _item.mandatory_code no # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail RMSD "clustered by RMSD" dRMSD "clustered by dRMSD" other "clustered by other feature" # save_ # save__ihm_ensemble_info.num_ensemble_models _item_description.description " The number of models in the current ensemble being described." # _item.name "_ihm_ensemble_info.num_ensemble_models" _item.category_id ihm_ensemble_info _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_ensemble_info.num_ensemble_models_deposited _item_description.description " The number of models from the current ensemble that is deposited." # _item.name "_ihm_ensemble_info.num_ensemble_models_deposited" _item.category_id ihm_ensemble_info _item.mandatory_code no # _item_type.code int # save_ # save__ihm_ensemble_info.ensemble_precision_value _item_description.description ; The precision of each cluster or ensemble is calculated as dRMSD, which is the average C-alpha distance root mean square deviation (dRMSD) between the individual models in the cluster and the cluster centroid. The cluster centroid is defined as the model with the minimal sum of dRMSDs to the other models in the cluster or ensemble. ; # _item.name "_ihm_ensemble_info.ensemble_precision_value" _item.category_id ihm_ensemble_info _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_ensemble_info.ensemble_file_id _item_description.description ; A reference to the external file containing the structural models in the ensemble. The number of models in the external file should correspond to the number of models in the ensemble. This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES category. It is recommended that the large ensemble files be stored as separate zip files within the same DOI. It is also recommended that large sphere model ensembles be in binary format, which facilitates faster access. Currently, a binary dump of co-ordinates in dcd format is suggested. The topology can be inferred from the IHM_SPHERE_OBJ_SITE and the ATOM_SITE categories in the corresponding mmCIF file. ; # _item.name "_ihm_ensemble_info.ensemble_file_id" _item.category_id ihm_ensemble_info _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_ensemble_info.ensemble_file_id" _item_linked.parent_name "_ihm_external_files.id" # save_ # save__ihm_ensemble_info.details _item_description.description " Additional details regarding the ensemble." # _item.name "_ihm_ensemble_info.details" _item.category_id ihm_ensemble_info _item.mandatory_code no # _item_type.code text # save_ # save__ihm_ensemble_info.sub_sample_flag _item_description.description " Indicate if the ensemble consists of sub samples." # _item.name "_ihm_ensemble_info.sub_sample_flag" _item.category_id ihm_ensemble_info _item.mandatory_code no # _item_type.code ucode # loop_ _item_enumeration.value YES NO # save_ # save__ihm_ensemble_info.sub_sampling_type _item_description.description " Indicate the sub sampling type, if applicable." # _item.name "_ihm_ensemble_info.sub_sampling_type" _item.category_id ihm_ensemble_info _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail random "sub samples generated by randomly partitioning all structures in the group" independent "each sub sample generated in the same fashion but in independent simulations" other "other type of sub sampling" # save_ # save_ihm_ensemble_sub_sample _category.description ; Data items in the IHM_ENSEMBLE_SUB_SAMPLE category records the details of the sub samples within the ensembles. ; _category.id ihm_ensemble_sub_sample _category.mandatory_code no # _category_key.name "_ihm_ensemble_sub_sample.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_ensemble_sub_sample.id _ihm_ensemble_sub_sample.name _ihm_ensemble_sub_sample.ensemble_id _ihm_ensemble_sub_sample.num_models _ihm_ensemble_sub_sample.num_models_deposited _ihm_ensemble_sub_sample.model_group_id _ihm_ensemble_sub_sample.file_id 1 'sub sample 1' 1 500 2 1 24 2 'sub sample 2' 1 500 2 2 25 3 'sub sample 3' 2 500 2 3 26 4 'sub sample 4' 2 500 2 4 27 ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_ensemble_sub_sample # save_ # save__ihm_ensemble_sub_sample.id _item_description.description " A unique id for the ensemble sub sample." # _item.name "_ihm_ensemble_sub_sample.id" _item.category_id ihm_ensemble_sub_sample _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_ensemble_sub_sample.name _item_description.description " A name for the ensemble sub sample." # _item.name "_ihm_ensemble_sub_sample.name" _item.category_id ihm_ensemble_sub_sample _item.mandatory_code no # _item_type.code line # save_ # save__ihm_ensemble_sub_sample.ensemble_id _item_description.description ; The ensemble identifier corresponding to the sub sample. This data item is a pointer to _ihm_ensemble_info.ensemble_id in the IHM_ENSEMBLE_INFO category. ; # _item.name "_ihm_ensemble_sub_sample.ensemble_id" _item.category_id ihm_ensemble_sub_sample _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_ensemble_sub_sample.ensemble_id" _item_linked.parent_name "_ihm_ensemble_info.ensemble_id" # save_ # save__ihm_ensemble_sub_sample.num_models _item_description.description " The number of models in the ensemble sub sample." # _item.name "_ihm_ensemble_sub_sample.num_models" _item.category_id ihm_ensemble_sub_sample _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_ensemble_sub_sample.num_models_deposited _item_description.description " The number of models in the sub sample that are deposited." # _item.name "_ihm_ensemble_sub_sample.num_models_deposited" _item.category_id ihm_ensemble_sub_sample _item.mandatory_code no # _item_type.code int # save_ # save__ihm_ensemble_sub_sample.model_group_id _item_description.description ; The model group identifier corresponding to the sub sample, if applicable. This data item is a pointer to _ihm_model_group.id in the IHM_MODEL_GROUP category. ; # _item.name "_ihm_ensemble_sub_sample.model_group_id" _item.category_id ihm_ensemble_sub_sample _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_ensemble_sub_sample.model_group_id" _item_linked.parent_name "_ihm_model_group.id" # save_ # save__ihm_ensemble_sub_sample.file_id _item_description.description ; A reference to the external file containing the structural models in the sub sample. The number of models in the external file should correspond to the number of models in the sub sample. This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES category. ; # _item.name "_ihm_ensemble_sub_sample.file_id" _item.category_id ihm_ensemble_sub_sample _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_ensemble_sub_sample.file_id" _item_linked.parent_name "_ihm_external_files.id" # save_ # save_ihm_model_list _category.description ; Data items in the IHM_MODEL_LIST category record the details of the models being deposited. ; _category.id ihm_model_list _category.mandatory_code no # _category_key.name "_ihm_model_list.model_id" # loop_ _category_group.id inclusive_group ihm_group # loop_ _category_examples.detail _category_examples.case ; Example 1 - ; ; loop_ _ihm_model_list.model_id _ihm_model_list.model_name _ihm_model_list.assembly_id _ihm_model_list.protocol_id _ihm_model_list.representation_id 1 'Best scoring model' 1 1 1 2 '2nd Best scoring model' 1 1 1 3 '3rd Best scoring model' 1 1 1 4 '4th Best scoring model' 1 1 1 5 '5th Best scoring model' 1 1 1 # ... abbreviated ... ; ; Example 2 - ; ; loop_ _ihm_model_list.model_id _ihm_model_list.model_name _ihm_model_list.assembly_id _ihm_model_list.protocol_id _ihm_model_list.representation_id 1 'Best scoring model, open state' 1 1 1 2 '2nd best scoring model, open state' 1 1 1 3 '3rd best scoring model, open state' 1 1 1 4 '4th best scoring model, open state' 1 1 1 5 '5th best scoring model, open state' 1 1 1 6 'Best scoring model, closed state' 1 1 1 7 '2nd best scoring model, closed state' 1 1 1 8 '3rd best scoring model, closed state' 1 1 1 9 '4th best scoring model, closed state' 1 1 1 10 '5th best scoring model, closed state' 1 1 1 # ... abbreviated ... ; ; Example 3 - ; ; loop_ _ihm_model_list.model_id _ihm_model_list.model_name _ihm_model_list.assembly_id _ihm_model_list.protocol_id _ihm_model_list.representation_id 1 'Best scoring model, Bound state ensemble 1' 1 1 1 2 '2nd best scoring model, Bound state ensemble 1' 1 1 1 3 '3rd best scoring model, Bound state ensemble 1' 1 1 1 4 '4th best scoring model, Bound state ensemble 1' 1 1 1 5 '5th best scoring model, Bound state ensemble 1' 1 1 1 6 'Best scoring model, Unbound state ensemble 2' 2 1 2 7 '2nd best scoring model, Unbound state ensemble 2' 2 1 2 8 '3rd best scoring model, Unbound state ensemble 2' 2 1 2 9 '4th best scoring model, Unbound state ensemble 2' 2 1 2 10 '5th best scoring model, Unbound state ensemble 2' 2 1 2 # ... abbreviated ... ; ; Example 4 - Multi-scale, multi-state and time-ordered ensemble ; ; loop_ _ihm_model_list.model_id _ihm_model_list.model_name _ihm_model_list.assembly_id _ihm_model_list.protocol_id _ihm_model_list.representation_id 1 'Best scoring model, open state, time step 1' 1 1 1 2 '2nd Best scoring model, open state, time step 1' 1 1 1 3 'Best scoring model, closed state, time step 1' 1 1 1 4 '2nd Best scoring model, closed state, time step 1' 1 1 1 5 'Best scoring model, open state, time step 2' 1 1 1 6 '2nd Best scoring model, open state, time step 2' 1 1 1 7 'Best scoring model, closed state, time step 2' 1 1 1 8 '2nd Best scoring model, closed state, time step 2' 1 1 1 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_model_list # save_ # save__ihm_model_list.model_id _item_description.description " A unique identifier for the structural model being deposited." # _item.name "_ihm_model_list.model_id" _item.category_id ihm_model_list _item.mandatory_code yes # _item_type.code int # _item_linked.parent_name "_ihm_model_list.model_id" _item_linked.child_name "_atom_site.pdbx_PDB_model_num" # save_ # save__ihm_model_list.model_name _item_description.description " A decsriptive name for the model." # _item.name "_ihm_model_list.model_name" _item.category_id ihm_model_list _item.mandatory_code no # _item_type.code line # loop_ _item_examples.case "Best scoring model" "2nd best scoring model" "Cluster center" # save_ # save__ihm_model_list.assembly_id _item_description.description ; An identifier to the structure assembly corresponding to the model. This data item is a pointer to the _ihm_struct_assembly.id in the IHM_STRUCT_ASSEMBLY category. ; # _item.name "_ihm_model_list.assembly_id" _item.category_id ihm_model_list _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_model_list.assembly_id" _item_linked.parent_name "_ihm_struct_assembly.id" # save_ # save__ihm_model_list.protocol_id _item_description.description ; An identifier to the modeling protocol that produced the model. This data item is a pointer to the _ihm_modeling_protocol.id in the IHM_MODELING_PROTOCOL category. ; # _item.name "_ihm_model_list.protocol_id" _item.category_id ihm_model_list _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_model_list.protocol_id" _item_linked.parent_name "_ihm_modeling_protocol.id" # save_ # save__ihm_model_list.representation_id _item_description.description ; An identifier to the multi-scale model representation id of the model. This data item is a pointer to the _ihm_model_representation.id in the IHM_MODEL_REPRESENTATION category. ; # _item.name "_ihm_model_list.representation_id" _item.category_id ihm_model_list _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_model_list.representation_id" _item_linked.parent_name "_ihm_model_representation.id" # save_ # save_ihm_model_group _category.description ; IHM_MODEL_GROUP category defines collections or groups of integrative structural models. ; _category.id ihm_model_group _category.mandatory_code no # _category_key.name "_ihm_model_group.id" # loop_ _category_group.id inclusive_group ihm_group # loop_ _category_examples.detail _category_examples.case ; Example 1 - ; ; loop_ _ihm_model_group.id _ihm_model_group.name _ihm_model_group.details 1 'Open state' 'Ensemble of open state models' 2 'Closed state' 'Ensemble of closed state models' ; ; Example 2 - ; ; loop_ _ihm_model_group.id _ihm_model_group.name _ihm_model_group.details 1 'Open State in time step 1' 'Ensemble of open state models in time step 1' 2 'Open State in time step 2' 'Ensemble of open state models in time step 2' 3 'Closed State in time step 1' 'Ensemble of closed state models in time step 1' 4 'Closed State in time step 2' 'Ensemble of closed state models in time step 2' ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_model_group # save_ # save__ihm_model_group.id _item_description.description ; A unique identifier for a collection or group of structural models. This data item can be used to group models into structural clusters or using other criteria based on experimental data or other relationships such as those belonging to the same state or time stamp. An ensemble of models and its representative can either be grouped together or can be separate groups in the ihm_model_group table. The choice between the two options should be decided based on how the modeling was carried out and how the representative was chosen. If the representative is a member of the ensemble (i.e., best scoring model), then it is recommended that the representative and the ensemble belong to the same model group. If the representative is calculated from the ensemble (i.e., centroid), then it is recommended that the representative be separated into a different group. ; # _item.name "_ihm_model_group.id" _item.category_id ihm_model_group _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_model_group.name _item_description.description " A name for the collection of models." # _item.name "_ihm_model_group.name" _item.category_id ihm_model_group _item.mandatory_code no # _item_type.code line # loop_ _item_examples.case cluster1 cluster2 ensemble1 ensemble2 "open state" "closed state" "bound state" "unbound state" "bound state ensemble 1" "unbound state ensemble 2" # save_ # save__ihm_model_group.details _item_description.description " Additional details about the collection of models." # _item.name "_ihm_model_group.details" _item.category_id ihm_model_group _item.mandatory_code no # _item_type.code text # save_ # save_ihm_model_group_link _category.description ; IHM_MODEL_GROUP_LINK category provides the list of models present in a particular model group. ; _category.id ihm_model_group_link _category.mandatory_code no # loop_ _category_key.name "_ihm_model_group_link.model_id" "_ihm_model_group_link.group_id" # loop_ _category_group.id inclusive_group ihm_group # loop_ _category_examples.detail _category_examples.case ; Example 1 - Same model in multiple groups ; ; loop_ _ihm_model_group_link.model_id _ihm_model_group_link.group_id 1 1 2 1 3 1 4 1 5 1 1 2 2 2 3 2 4 3 5 3 ; ; Example 2 - Each model in an independent group ; ; loop_ _ihm_model_group_link.model_id _ihm_model_group_link.group_id 1 1 2 2 3 3 4 4 5 5 ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_model_group_link # save_ # save__ihm_model_group_link.model_id _item_description.description ; An identifier for the structural model. This data item is a pointer to _ihm_model_list.model_id in the IHM_MODEL_LIST category. ; # _item.name "_ihm_model_group_link.model_id" _item.category_id ihm_model_group_link _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_model_group_link.model_id" _item_linked.parent_name "_ihm_model_list.model_id" # save_ # save__ihm_model_group_link.group_id _item_description.description ; An identifier for the structural model group. This data item is a pointer to _ihm_model_group.id in the IHM_MODEL_GROUP category. ; # _item.name "_ihm_model_group_link.group_id" _item.category_id ihm_model_group_link _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_model_group_link.group_id" _item_linked.parent_name "_ihm_model_group.id" # save_ # save_ihm_model_representative _category.description ; Data items in the IHM_MODEL_REPRESENTATIVE category record the details of the representative model in an ensemble or cluster. ; _category.id ihm_model_representative _category.mandatory_code no # _category_key.name "_ihm_model_representative.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_model_representative.id _ihm_model_representative.model_group_id _ihm_model_representative.model_id _ihm_model_representative.selection_criteria 1 1 1 'best scoring model' 2 1 2 'medioid' 3 2 6 'best scoring model' 4 2 7 'medioid' #...abbreviated...# ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_model_representative # save_ # save__ihm_model_representative.id _item_description.description " A unique identifier for the representative of the model group." # _item.name "_ihm_model_representative.id" _item.category_id ihm_model_representative _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_model_representative.model_group_id _item_description.description ; The model group identifier corresponding to the representative model. This data item is a pointer to _ihm_model_group.id in the IHM_MODEL_GROUP category. ; # _item.name "_ihm_model_representative.model_group_id" _item.category_id ihm_model_representative _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_model_representative.model_group_id" _item_linked.parent_name "_ihm_model_group.id" # save_ # save__ihm_model_representative.model_id _item_description.description ; The model identifier corresponding to the representative model. This data item is a pointer to _ihm_model_list.model_id in the IHM_MODEL_LIST category. ; # _item.name "_ihm_model_representative.model_id" _item.category_id ihm_model_representative _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_model_representative.model_id" _item_linked.parent_name "_ihm_model_list.model_id" # save_ # save__ihm_model_representative.selection_criteria _item_description.description " The selection criteria based on which the representative is chosen." # _item.name "_ihm_model_representative.selection_criteria" _item.category_id ihm_model_representative _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail medoid "most similar to other models" "closest to the average" . "lowest energy" . "target function" . "fewest violations" . "minimized average structure" . "best scoring model" . centroid "centroid of a cluster" "other selction criteria" . # save_ # save__atom_site.ihm_model_id _item_description.description ; The model id corresponding to the atom site. This data item is a pointer to _ihm_model_list.model_id in the IHM_MODEL_LIST category. ; # _item.name "_atom_site.ihm_model_id" _item.category_id atom_site _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_atom_site.ihm_model_id" _item_linked.parent_name "_ihm_model_list.model_id" # save_ # save_ihm_dataset_list _category.description ; Category holds the list of all datasets used in the IHM modeling. These can be datasets archived in other related databases such as BMRB, EMDB, EMPIAR, SASBDB, PRIDE etc., or can be hosted in other places such as the authors website, github etc. These datasets are elaborated in detail in the IHM_DATASET_RELATED_DB_REFERENCE and/or the IHM_DATASET_EXTERNAL_REFERENCE categories. This category holds the list of all datasets used. ; _category.id ihm_dataset_list _category.mandatory_code no # _category_key.name "_ihm_dataset_list.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 ; _category_examples.case ; loop_ _ihm_dataset_list.id _ihm_dataset_list.data_type _ihm_dataset_list.database_hosted 1 'CX-MS data' 'NO' 2 'CX-MS data' 'NO' 3 '3DEM volume' 'YES' 4 '2DEM class average' 'NO' 5 'Comparative model' 'NO' 6 'EM raw micrographs' 'NO' # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_dataset_list # save_ # save__ihm_dataset_list.id _item_description.description " A unique identifier for the dataset." # _item.name "_ihm_dataset_list.id" _item.category_id ihm_dataset_list _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_dataset_list.data_type _item_description.description " The type of data held in the dataset." # _item.name "_ihm_dataset_list.data_type" _item.category_id ihm_dataset_list _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value "NMR data" "3DEM volume" "2DEM class average" "EM raw micrographs" "X-ray diffraction data" "SAS data" "CX-MS data" "Mass Spectrometry data" "EPR data" "H/D exchange data" "Single molecule FRET data" "Ensemble FRET data" "Experimental model" "Comparative model" "Integrative model" "De Novo model" "Predicted contacts" "Mutagenesis data" "DNA footprinting data" "Hydroxyl radical footprinting data" "Yeast two-hybrid screening data" "Quantitative measurements of genetic interactions" Other # save_ # save__ihm_dataset_list.details _item_description.description ; Details regarding the dataset, especially those types not listed in _ihm_dataset_list.data_type. ; # _item.name "_ihm_dataset_list.details" _item.category_id ihm_dataset_list _item.mandatory_code no # _item_type.code text # save_ # save__ihm_dataset_list.database_hosted _item_description.description ; A flag that indicates whether the dataset is archived in an IHM related database or elsewhere. ; # _item.name "_ihm_dataset_list.database_hosted" _item.category_id ihm_dataset_list _item.mandatory_code yes # _item_type.code ucode # loop_ _item_enumeration.value YES NO # save_ # save_ihm_dataset_group _category.description " Category to define groups or collections of input datasets." _category.id ihm_dataset_group _category.mandatory_code no # _category_key.name "_ihm_dataset_group.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 ; _category_examples.case ; loop_ _ihm_dataset_group.id _ihm_dataset_group.name _ihm_dataset_group.application _ihm_dataset_group.details 1 'Experimental data' 'validation' . 2 'Starting structural models' 'restraint' . 3 'Comparative model templates' 'representation' . 4 'Input data for docking' 'restraint' . 5 'Input data for integrative modeling' 'restraint' . # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_dataset_group # save_ # save__ihm_dataset_group.id _item_description.description " A unique identifier for the dataset group." # _item.name "_ihm_dataset_group.id" _item.category_id ihm_dataset_group _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_dataset_group.name _item_description.description " A name for the dataset group." # _item.name "_ihm_dataset_group.name" _item.category_id ihm_dataset_group _item.mandatory_code no # _item_type.code line # save_ # save__ihm_dataset_group.application _item_description.description " The application / utilization of the dataset group in modeling." # _item.name "_ihm_dataset_group.application" _item.category_id ihm_dataset_group _item.mandatory_code no # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail restraint "dataset used as input spatial restraints in modeling" validation "dataset used for validation" filter "dataset used for filtering sampled models" representation "dataset used in model representation" sampling "dataset used to bias sampling" other "dataset used in other ways" # save_ # save__ihm_dataset_group.details _item_description.description " Additional details regarding the dataset group." # _item.name "_ihm_dataset_group.details" _item.category_id ihm_dataset_group _item.mandatory_code no # _item_type.code text # save_ # save_ihm_dataset_group_link _category.description ; IHM_DATASET_GROUP_LINK category provides the list of datasets present in a particular group. ; _category.id ihm_dataset_group_link _category.mandatory_code no # loop_ _category_key.name "_ihm_dataset_group_link.dataset_list_id" "_ihm_dataset_group_link.group_id" # loop_ _category_group.id inclusive_group ihm_group # loop_ _category_examples.detail _category_examples.case ; Example 1 - Same dataset in multiple groups ; ; loop_ _ihm_dataset_group_link.dataset_list_id _ihm_dataset_group_link.group_id 1 1 2 1 3 1 4 1 5 1 1 2 2 2 3 2 ; ; Example 2 - Each dataset in an independent group ; ; loop_ _ihm_dataset_group_link.dataset_list_id _ihm_dataset_group_link.group_id 1 1 2 2 3 3 4 4 5 5 ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_dataset_group_link # save_ # save__ihm_dataset_group_link.dataset_list_id _item_description.description ; An identifier for the dataset. This data item is a pointer to _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_dataset_group_link.dataset_list_id" _item.category_id ihm_dataset_group_link _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_dataset_group_link.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save__ihm_dataset_group_link.group_id _item_description.description ; An identifier for the dataset group. This data item is a pointer to _ihm_dataset_group.id in the IHM_DATASET_GROUP category. ; # _item.name "_ihm_dataset_group_link.group_id" _item.category_id ihm_dataset_group_link _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_dataset_group_link.group_id" _item_linked.parent_name "_ihm_dataset_group.id" # save_ # save_ihm_related_datasets _category.description " Category holds information about related datasets, where one is derived from the other." _category.id ihm_related_datasets _category.mandatory_code no # loop_ _category_key.name "_ihm_related_datasets.dataset_list_id_primary" "_ihm_related_datasets.dataset_list_id_derived" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 ; _category_examples.case ; loop_ _ihm_related_datasets.dataset_list_id_primary _ihm_related_datasets.dataset_list_id_derived 1 5 2 6 3 7 4 8 # ... abbreviated ... # ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_related_datasets # save_ # save__ihm_related_datasets.dataset_list_id_derived _item_description.description ; The dataset list id corresponding to the derived dataset. This data item is a pointer to _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_related_datasets.dataset_list_id_derived" _item.category_id ihm_related_datasets _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_related_datasets.dataset_list_id_derived" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save__ihm_related_datasets.dataset_list_id_primary _item_description.description ; The primary dataset list id from which the corresponding derived dataset is obtained. This data item is a pointer to _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_related_datasets.dataset_list_id_primary" _item.category_id ihm_related_datasets _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_related_datasets.dataset_list_id_primary" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save__ihm_related_datasets.transformation_id _item_description.description ; A pointer to the transformation matrix, if applicable. The transformation matrix is to be applied to the derived dataset in order to transform it to the primary dataset from which it is derived. Examples include segmented 3DEM maps, Gaussian Mixture Models derived from 3DEM maps, starting comparative models. This data item is a pointer to _ihm_data_transformation.id in the IHM_DATA_TRANSFORMATION category. ; # _item.name "_ihm_related_datasets.transformation_id" _item.category_id ihm_related_datasets _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_related_datasets.transformation_id" _item_linked.parent_name "_ihm_data_transformation.id" # save_ # save_ihm_data_transformation _category.description ; Data items in the IHM_DATA_TRANSFORMATION category records the details of the rotation matrix and translation vector that can be applied to transform the data. ; _category.id ihm_data_transformation _category.mandatory_code no # _category_key.name "_ihm_data_transformation.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; _ihm_data_transformation.id 1 _ihm_data_transformation.rot_matrix[1][1] 1.0 _ihm_data_transformation.rot_matrix[2][1] 0.0 _ihm_data_transformation.rot_matrix[3][1] 0.0 _ihm_data_transformation.rot_matrix[1][2] 0.0 _ihm_data_transformation.rot_matrix[2][2] 1.0 _ihm_data_transformation.rot_matrix[3][2] 0.0 _ihm_data_transformation.rot_matrix[1][3] 0.0 _ihm_data_transformation.rot_matrix[2][3] 0.0 _ihm_data_transformation.rot_matrix[3][3] 1.0 _ihm_data_transformation.tr_vector[1] 0.0 _ihm_data_transformation.tr_vector[2] 0.0 _ihm_data_transformation.tr_vector[3] 0.0 ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_data_transformation # save_ # save__ihm_data_transformation.id _item_description.description " A unique identifier for the transformation." # _item.name "_ihm_data_transformation.id" _item.category_id ihm_data_transformation _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_data_transformation.rot_matrix[1][1] _item_description.description " Data item [1][1] of the rotation matrix used in the transformation." # _item.name "_ihm_data_transformation.rot_matrix[1][1]" _item.category_id ihm_data_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_data_transformation.rot_matrix[2][1] _item_description.description " Data item [2][1] of the rotation matrix used in the transformation." # _item.name "_ihm_data_transformation.rot_matrix[2][1]" _item.category_id ihm_data_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_data_transformation.rot_matrix[3][1] _item_description.description " Data item [3][1] of the rotation matrix used in the transformation." # _item.name "_ihm_data_transformation.rot_matrix[3][1]" _item.category_id ihm_data_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_data_transformation.rot_matrix[1][2] _item_description.description " Data item [1][2] of the rotation matrix used in the transformation." # _item.name "_ihm_data_transformation.rot_matrix[1][2]" _item.category_id ihm_data_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_data_transformation.rot_matrix[2][2] _item_description.description " Data item [2][2] of the rotation matrix used in the transformation." # _item.name "_ihm_data_transformation.rot_matrix[2][2]" _item.category_id ihm_data_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_data_transformation.rot_matrix[3][2] _item_description.description " Data item [3][2] of the rotation matrix used in the transformation." # _item.name "_ihm_data_transformation.rot_matrix[3][2]" _item.category_id ihm_data_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_data_transformation.rot_matrix[1][3] _item_description.description " Data item [1][3] of the rotation matrix used in the transformation." # _item.name "_ihm_data_transformation.rot_matrix[1][3]" _item.category_id ihm_data_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_data_transformation.rot_matrix[2][3] _item_description.description " Data item [2][3] of the rotation matrix used in the transformation." # _item.name "_ihm_data_transformation.rot_matrix[2][3]" _item.category_id ihm_data_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_data_transformation.rot_matrix[3][3] _item_description.description " Data item [3][3] of the rotation matrix used in the transformation." # _item.name "_ihm_data_transformation.rot_matrix[3][3]" _item.category_id ihm_data_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_data_transformation.tr_vector[1] _item_description.description " Data item [1] of the translation vector used in the transformation." # _item.name "_ihm_data_transformation.tr_vector[1]" _item.category_id ihm_data_transformation _item.mandatory_code no # _item_sub_category.id vector # _item_type.code float # save_ # save__ihm_data_transformation.tr_vector[2] _item_description.description " Data item [2] of the translation vector used in the transformation." # _item.name "_ihm_data_transformation.tr_vector[2]" _item.category_id ihm_data_transformation _item.mandatory_code no # _item_sub_category.id vector # _item_type.code float # save_ # save__ihm_data_transformation.tr_vector[3] _item_description.description " Data item [3] of the translation vector used in the transformation." # _item.name "_ihm_data_transformation.tr_vector[3]" _item.category_id ihm_data_transformation _item.mandatory_code no # _item_sub_category.id vector # _item_type.code float # save_ # save_ihm_dataset_related_db_reference _category.description ; Category holds information related to data sources for the entry. These can be datasets archived in other related databases such as BMRB, EMDB, EMPIAR, SASBDB, PRIDE etc. ; _category.id ihm_dataset_related_db_reference _category.mandatory_code no # _category_key.name "_ihm_dataset_related_db_reference.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 ; _category_examples.case ; loop_ _ihm_dataset_related_db_reference.id _ihm_dataset_related_db_reference.dataset_list_id _ihm_dataset_related_db_reference.db_name _ihm_dataset_related_db_reference.accession_code _ihm_dataset_related_db_reference.version _ihm_dataset_related_db_reference.details 1 6 'PRIDE' 'PXD00381' . 'Structural Analysis of a Prokaryotic Ribosome Using a Novel Amidinating Cross-Linker and Mass Spectrometry' 2 3 'EMDB' 'EMD-2799' . . 3 5 'PDB' '5FM1' . 'STRUCTURE OF GAMMA-TUBULIN SMALL COMPLEX BASED ON A CRYO-EM MAP, CHEMICAL CROSS-LINKS, AND A REMOTELY RELATED STRUCTURE' 4 7 'BMRB' '25766' . . 5 8 'MODEL ARCHIVE' 'MA-CO2KC' . 'PREDICTED STRUCTURE OF AN ALPHA NEUROTOXIN FROM TAIWAN COBRA BY HOMOLOGY MODELING' # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_dataset_related_db_reference # save_ # save__ihm_dataset_related_db_reference.id _item_description.description " A unique identifier for the related database entry." # _item.name "_ihm_dataset_related_db_reference.id" _item.category_id ihm_dataset_related_db_reference _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_dataset_related_db_reference.dataset_list_id _item_description.description ; Identifier to the dataset list used in the IHM modeling. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_dataset_related_db_reference.dataset_list_id" _item.category_id ihm_dataset_related_db_reference _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_dataset_related_db_reference.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save__ihm_dataset_related_db_reference.db_name _item_description.description " The name of the database containing the dataset entry." # _item.name "_ihm_dataset_related_db_reference.db_name" _item.category_id ihm_dataset_related_db_reference _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value PDB PDB-Dev BMRB EMDB EMPIAR SASBDB PRIDE "MODEL ARCHIVE" MASSIVE BioGRID ProXL jPOSTrepo iProX AlphaFoldDB Other # save_ # save__ihm_dataset_related_db_reference.accession_code _item_description.description " The accession code for the database entry." # _item.name "_ihm_dataset_related_db_reference.accession_code" _item.category_id ihm_dataset_related_db_reference _item.mandatory_code yes # _item_type.code line # loop_ _item_examples.case 5FM1 25766 EMD-2799 10049 SASDA82 PXD003381 MA-CO2KC # save_ # save__ihm_dataset_related_db_reference.version _item_description.description " Version of the database entry, if the database allows versioning." # _item.name "_ihm_dataset_related_db_reference.version" _item.category_id ihm_dataset_related_db_reference _item.mandatory_code no # _item_type.code code # save_ # save__ihm_dataset_related_db_reference.details _item_description.description " Details regarding the dataset entry." # _item.name "_ihm_dataset_related_db_reference.details" _item.category_id ihm_dataset_related_db_reference _item.mandatory_code no # _item_type.code text # _item_examples.case "Structural Analysis of a Prokaryotic Ribosome Using a Novel Amidinating Cross-Linker and Mass Spectrometry" # save_ # save_ihm_external_reference_info _category.description ; Category holds links to other external data sources for the I/H model entry. Input datasets held in other databases such as EMDB, BMRB, SASBDB etc. are referenced in the IHM_DATASET_RELATED_DB_REFERENCE category. This data category, along with IHM_EXTERNAL_FILES category, holds information regarding other non-database external data sources, such as DOIs (digital object identifiers) or supplementary files stored locally. The DOIs can either lead to the external data file(s) directly (as in case of DOIs provided by the PDB) or might lead to an HTML landing page (as provided by Zenodo). In the latter case, additional URL (Uniform Resource Locator) information is required to retrieve the external data file(s). ; _category.id ihm_external_reference_info _category.mandatory_code no # _category_key.name "_ihm_external_reference_info.reference_id" # loop_ _category_group.id inclusive_group ihm_group # loop_ _category_examples.detail _category_examples.case ; Example 1 - DOI reference leading to an archive ; ; loop_ _ihm_external_reference_info.reference_id _ihm_external_reference_info.reference_provider _ihm_external_reference_info.reference_type _ihm_external_reference_info.reference _ihm_external_reference_info.refers_to _ihm_external_reference_info.associated_url 1 'Zenodo' 'DOI' '10.5281/zenodo.46266' 'Archive' 'https://zenodo.org/record/46266/files/nup84-v1.0.zip' # ... abbreviated ... ; ; Example 2 - Supplementary files stored locally ; ; _ihm_external_reference_info.reference_id 2 _ihm_external_reference_info.reference_type 'Supplementary Files' _ihm_external_reference_info.reference . _ihm_external_reference_info.refers_to 'Other' ; ; Example 3 - DOI reference leading to a single file ; ; loop_ _ihm_external_reference_info.reference_id _ihm_external_reference_info.reference_provider _ihm_external_reference_info.reference_type _ihm_external_reference_info.reference _ihm_external_reference_info.refers_to _ihm_external_reference_info.associated_url 3 'Zenodo' 'DOI' '10.5281/zenodo.58025' 'File' 'https://zenodo.org/record/58025/files/Nup84complex_particles.spd' # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_external_reference_info # save_ # save__ihm_external_reference_info.reference_id _item_description.description " A unique identifier for the external reference." # _item.name "_ihm_external_reference_info.reference_id" _item.category_id ihm_external_reference_info _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_external_reference_info.reference_provider _item_description.description " The name of the reference provider." # _item.name "_ihm_external_reference_info.reference_provider" _item.category_id ihm_external_reference_info _item.mandatory_code no # _item_type.code line # loop_ _item_examples.case Zenodo Figshare Crossref # save_ # save__ihm_external_reference_info.reference_type _item_description.description ; The type of external reference. Currently, only Digital Object Identifiers (DOIs) and supplementary files stored locally are supported. ; # _item.name "_ihm_external_reference_info.reference_type" _item.category_id ihm_external_reference_info _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail DOI "External reference is a Digital Object Identifier" "Supplementary Files" "External reference includes supplementary files stored locally" # save_ # save__ihm_external_reference_info.reference _item_description.description ; The external reference or the Digital Object Identifier (DOI). This field is not relevant for local files. ; # _item.name "_ihm_external_reference_info.reference" _item.category_id ihm_external_reference_info _item.mandatory_code yes # _item_type.code code # _item_examples.case 10.5281/zenodo.46266 # save_ # save__ihm_external_reference_info.refers_to _item_description.description ; The type of object that the external reference points to, usually a single file or an archive. ; # _item.name "_ihm_external_reference_info.refers_to" _item.category_id ihm_external_reference_info _item.mandatory_code yes # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail File "Refers to a single file" Archive "Refers to a tar and/or a compressed file" Publication "Refers to data from previously published work" Other "Other kind of object" # save_ # save__ihm_external_reference_info.associated_url _item_description.description ; The Uniform Resource Locator (URL) corresponding to the external reference (DOI). This URL should link to the corresponding downloadable file or archive and is provided to enable automated software to download the referenced file or archive. ; # _item.name "_ihm_external_reference_info.associated_url" _item.category_id ihm_external_reference_info _item.mandatory_code no # _item_type.code code # save_ # save__ihm_external_reference_info.details _item_description.description " Additional details regarding the external reference." # _item.name "_ihm_external_reference_info.details" _item.category_id ihm_external_reference_info _item.mandatory_code no # _item_type.code text # save_ # save_ihm_external_files _category.description ; Category provides details regarding external files. The IHM_EXTERNAL_REFERENCE_INFO category captures the top-level details regarding external data sources. This category captures the specific details regarding externally stored files related to the particular I/H model entry. ; _category.id ihm_external_files _category.mandatory_code no # _category_key.name "_ihm_external_files.id" # loop_ _category_group.id inclusive_group ihm_group # loop_ _category_examples.detail _category_examples.case ; Example 1 - DOI Archive Files ; ; loop_ _ihm_external_files.id _ihm_external_files.reference_id _ihm_external_files.file_path _ihm_external_files.file_format _ihm_external_files.content_type _ihm_external_files.file_size_bytes _ihm_external_files.details 1 1 'integrativemodeling-nup84-a69f895/data/EDC_XL_122013.new.dat' 'TXT' 'Input data or restraints' . 'EDC crosslinks file' 2 1 'integrativemodeling-nup84-a69f895/data/yeast_Nup84_DSS.new.dat' 'TXT' 'Input data or restraints' . 'DSS crosslinks file' 3 1 'integrativemodeling-nup84-a69f895/data/nup84_kinked_from_class2.pgm' 'PGM' 'Input data or restraints' . 'Nup84 2DEM class average' 4 1 'integrativemodeling-nup84-a69f895/data/nup84_kinked_from_class2.mrc' 'MRC' 'Input data or restraints' . 'Nup84 2DEM class average' 5 1 'integrativemodeling-nup84-a69f895/data/ScSec13_2-296_new2.pdb' 'PDB' 'Input data or restraints' . 'Sec13 starting comparative model' 6 1 'integrativemodeling-nup84-a69f895/scripts/MODELLER_scripts/Nup84/all_align_final2.ali' 'PIR/NBRF' 'Input data or restraints' . 'Nup84 multiple sequence alignment file' 7 1 'integrativemodeling-nup84-a69f895/scripts/MODELLER_scripts/Nup84/all_align_final1.ali' 'PIR/NBRF' 'Input data or restraints' . 'Nup84 multiple sequence alignment file' 8 1 'integrativemodeling-nup84-a69f895/scripts/nup84.isd.modeling.py' 'Other' 'Modeling workflow or script' . 'Python integrative modeling main script' 9 1 'integrativemodeling-nup84-a69f895/scripts/nup84.topology.py' 'Other' 'Modeling workflow or script' . 'Python script for constructing subunits' 10 1 'integrativemodeling-nup84-a69f895/scripts/nup84.merge.py' 'Other' 'Modeling workflow or script' . 'Python script to merge output files' 11 1 'integrativemodeling-nup84-a69f895/scripts/README' 'TXT' 'Modeling workflow or script' . 'Readme file' 12 1 'integrativemodeling-nup84-a69f895/outputs/localization/cluster1/nup84.mrc' 'MRC' 'Modeling or post-processing output' . 'Nup84 localization density file' 13 1 'integrativemodeling-nup84-a69f895/outputs/localization/cluster1/nup85.mrc' 'MRC' 'Modeling or post-processing output' . 'Nup85 localization density file' 14 1 'integrativemodeling-nup84-a69f895/outputs/localization/cluster1/nup120.mrc' 'MRC' 'Modeling or post-processing output' . 'Nup120 localization density file' # ... abbreviated ... ; ; Example 2 - Supplementary Local Files ; ; loop_ _ihm_external_files.id _ihm_external_files.reference_id _ihm_external_files.file_path _ihm_external_files.file_format _ihm_external_files.content_type _ihm_external_files.file_size_bytes _ihm_external_files.details 1 2 'data/EDC_XL_122013.dat' 'TXT' 'Input data or restraints' . 'EDC crosslinks file' 2 2 'data/yeast_Nup84_DSS.dat' 'TXT' 'Input data or restraints' . 'DSS crosslinks file' 3 2 'nup145.mrc' 'MRC' 'Modeling or post-processing output' . 'Nup145 localization density file' # ... abbreviated ... ; ; Example 3 - DOI reference leading to a single file or data from previously published work ; ; loop_ _ihm_external_files.id _ihm_external_files.reference_id _ihm_external_files.file_path _ihm_external_files.content_type _ihm_external_files.details 1 3 . 'Input data or restraints' 'Raw micrographs from which the class average was derived' # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_external_files # save_ # save__ihm_external_files.id _item_description.description " A unique identifier for each external file." # _item.name "_ihm_external_files.id" _item.category_id ihm_external_files _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_external_files.reference_id _item_description.description ; A pointer to the source of the external file - either DOI or locally stored. This data item is a pointer to _ihm_external_reference_info.reference_id in the IHM_EXTERNAL_REFERENCE_INFO category. ; # _item.name "_ihm_external_files.reference_id" _item.category_id ihm_external_files _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_external_files.reference_id" _item_linked.parent_name "_ihm_external_reference_info.reference_id" # save_ # save__ihm_external_files.file_path _item_description.description ; The relative path (including filename) for each external file. Absolute paths (starting with "/") are not permitted. This is required for identifying individual files from within a tar-zipped archive file or for identifying supplementary local files organized within a directory structure. This data item assumes a POSIX-like directory structure or file path. ; # _item.name "_ihm_external_files.file_path" _item.category_id ihm_external_files _item.mandatory_code no # _item_type.code line # loop_ _item_examples.case integrativemodeling-nup84-a69f895/outputs/localization/cluster1/nup84.mrc integrativemodeling-nup84-a69f895/scripts/MODELLER_scripts/Nup84/all_align_final2.ali nup145.mrc data/EDC_XL_122013.dat # save_ # save__ihm_external_files.file_format _item_description.description " Format of the external file." # _item.name "_ihm_external_files.file_format" _item.category_id ihm_external_files _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value TXT PGM JPG GIF TIF PNG MRC CCP4 PDB CIF HDF5 DCD FASTA CLUSTALW PIR/NBRF A2M A3M PDF Other # save_ # save__ihm_external_files.content_type _item_description.description " The type of content in the file." # _item.name "_ihm_external_files.content_type" _item.category_id ihm_external_files _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value "Input data or restraints" "Modeling or post-processing output" "Modeling workflow or script" "Visualization script" Other # save_ # save__ihm_external_files.file_size_bytes _item_description.description " Storage size of the external file in bytes." # _item.name "_ihm_external_files.file_size_bytes" _item.category_id ihm_external_files _item.mandatory_code no # _item_type.code float # save_ # save__ihm_external_files.details _item_description.description " Additional textual details regarding the external file." # _item.name "_ihm_external_files.details" _item.category_id ihm_external_files _item.mandatory_code no # _item_type.code text # loop_ _item_examples.case "Readme file" "Nup84 multiple sequence alignment file" "Nup84 starting comparative model file" # save_ # save_ihm_dataset_external_reference _category.description ; Category provides additional details regarding input data hosted externally at other resources. ; _category.id ihm_dataset_external_reference _category.mandatory_code no # _category_key.name "_ihm_dataset_external_reference.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_dataset_external_reference.id _ihm_dataset_external_reference.dataset_list_id _ihm_dataset_external_reference.file_id 1 1 1 2 2 2 3 4 3 4 4 4 5 5 5 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_dataset_external_reference # save_ # save__ihm_dataset_external_reference.id _item_description.description " A unique identifier for the external data." # _item.name "_ihm_dataset_external_reference.id" _item.category_id ihm_dataset_external_reference _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_dataset_external_reference.dataset_list_id _item_description.description ; Identifier to the dataset list used in the I/H modeling. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_dataset_external_reference.dataset_list_id" _item.category_id ihm_dataset_external_reference _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_dataset_external_reference.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save__ihm_dataset_external_reference.file_id _item_description.description ; The file id corresponding to this external data file. This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES category. ; # _item.name "_ihm_dataset_external_reference.file_id" _item.category_id ihm_dataset_external_reference _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_dataset_external_reference.file_id" _item_linked.parent_name "_ihm_external_files.id" # save_ # save_ihm_localization_density_files _category.description ; Data items in the IHM_LOCALIZATION_DENSITY_FILES category records the details of files that provide information regarding localization densities of ensembles. These may be stored externally as local files or linked via DOI and can be in any accepted format that provides volume information (CCP4, MRC, etc.). ; _category.id ihm_localization_density_files _category.mandatory_code no # _category_key.name "_ihm_localization_density_files.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_localization_density_files.id _ihm_localization_density_files.file_id _ihm_localization_density_files.ensemble_id _ihm_localization_density_files.entity_id _ihm_localization_density_files.asym_id _ihm_localization_density_files.entity_poly_segment_id 1 12 1 1 A 1 2 13 1 2 B 2 3 14 1 3 C 3 # ...abbreviated... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_localization_density_files # save_ # save__ihm_localization_density_files.id _item_description.description " A unique identifier." # _item.name "_ihm_localization_density_files.id" _item.category_id ihm_localization_density_files _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_localization_density_files.file_id _item_description.description ; The file id for the externally stored localization density file. This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES category. ; # _item.name "_ihm_localization_density_files.file_id" _item.category_id ihm_localization_density_files _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_localization_density_files.file_id" _item_linked.parent_name "_ihm_external_files.id" # save_ # save__ihm_localization_density_files.ensemble_id _item_description.description ; The ensemble identifier for the ensemble, for which the localization density is provided. This data item is a pointer to _ihm_ensemble_info.ensemble_id in the IHM_ENSEMBLE_INFO category. ; # _item.name "_ihm_localization_density_files.ensemble_id" _item.category_id ihm_localization_density_files _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_localization_density_files.ensemble_id" _item_linked.parent_name "_ihm_ensemble_info.ensemble_id" # save_ # save__ihm_localization_density_files.entity_id _item_description.description ; The entity identifier corresponding to this localization density. This data item is a pointer to _entity.id in the ENTITY category. ; # _item.name "_ihm_localization_density_files.entity_id" _item.category_id ihm_localization_density_files _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_ihm_localization_density_files.entity_id" _item_linked.parent_name "_entity.id" # save_ # save__ihm_localization_density_files.entity_poly_segment_id _item_description.description ; The identifier for the polymeric segment corresponding to this localization density. This data item is a pointer to _ihm_entity_poly_segment.id in the IHM_ENTITY_POLY_SEGMENT category. ; # _item.name "_ihm_localization_density_files.entity_poly_segment_id" _item.category_id ihm_localization_density_files _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_localization_density_files.entity_poly_segment_id" _item_linked.parent_name "_ihm_entity_poly_segment.id" # save_ # save__ihm_localization_density_files.asym_id _item_description.description ; An asym/strand identifier corresponding to this localization density. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_localization_density_files.asym_id" _item.category_id ihm_localization_density_files _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_ihm_localization_density_files.asym_id" _item_linked.parent_name "_struct_asym.id" # save_ # save_ihm_predicted_contact_restraint _category.description ; Data items in the IHM_PREDICTED_CONTACT_RESTRAINT category records the list of predicted contacts used in the integrative modeling experiment. This has been adapted from the widely used CASP RR format (http://www.predictioncenter.org/casp8/index.cgi?page=format#RR). These contacts may be derived from various computational tools. The software information can be provided in the SOFTWARE category. ; _category.id ihm_predicted_contact_restraint _category.mandatory_code no # _category_key.name "_ihm_predicted_contact_restraint.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_predicted_contact_restraint.id _ihm_predicted_contact_restraint.entity_id_1 _ihm_predicted_contact_restraint.asym_id_1 _ihm_predicted_contact_restraint.seq_id_1 _ihm_predicted_contact_restraint.comp_id_1 _ihm_predicted_contact_restraint.rep_atom_1 _ihm_predicted_contact_restraint.entity_id_2 _ihm_predicted_contact_restraint.asym_id_2 _ihm_predicted_contact_restraint.seq_id_2 _ihm_predicted_contact_restraint.comp_id_2 _ihm_predicted_contact_restraint.rep_atom_2 _ihm_predicted_contact_restraint.restraint_type _ihm_predicted_contact_restraint.distance_upper_limit _ihm_predicted_contact_restraint.probability _ihm_predicted_contact_restraint.model_granularity _ihm_predicted_contact_restraint.dataset_list_id _ihm_predicted_contact_restraint.software_id 1 3 C 17 LYS CB 3 C 421 GLU CB 'upper bound' 8.0 0.8 'by-atom' 1 1 2 3 C 206 LYS CB 3 C 219 ASP CB 'upper bound' 8.0 0.5 'by-atom' 1 1 3 3 C 38 LYS CB 3 C 429 GLU CB 'upper bound' 8.0 0.8 'by-atom' 1 1 4 3 C 400 LYS CB 3 C 440 GLU CB 'upper bound' 8.0 0.6 'by-atom' 1 1 5 3 C 400 LYS CB 3 C 441 GLU CB 'upper bound' 8.0 0.7 'by-atom' 1 1 6 3 C 400 LYS CB 3 C 523 ASP CB 'upper bound' 8.0 0.7 'by-atom' 1 1 7 3 C 735 LYS CB 3 C 403 ASP CB 'upper bound' 8.0 0.5 'by-atom' 1 1 8 3 C 735 LYS CB 3 C 405 GLU CB 'upper bound' 8.0 0.5 'by-atom' 1 1 9 3 C 865 LYS CB 3 C 894 GLU CB 'upper bound' 8.0 0.9 'by-atom' 1 1 10 3 C 865 LYS CB 3 C 898 ASP CB 'upper bound' 8.0 0.5 'by-atom' 1 1 11 4 D 103 LYS CB 4 D 130 ASP CB 'upper bound' 8.0 0.7 'by-atom' 1 1 12 4 D 103 LYS CB 4 D 131 GLU CB 'upper bound' 8.0 0.3 'by-atom' 1 1 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_predicted_contact_restraint # save_ # save__ihm_predicted_contact_restraint.id _item_description.description " A unique identifier for the predicted contact restraint." # _item.name "_ihm_predicted_contact_restraint.id" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_predicted_contact_restraint.group_id _item_description.description " An identifier to group the predicted contacts." # _item.name "_ihm_predicted_contact_restraint.group_id" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code no # _item_type.code int # save_ # save__ihm_predicted_contact_restraint.entity_description_1 _item_description.description ; A text description of molecular entity 1. ; # _item.name "_ihm_predicted_contact_restraint.entity_description_1" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code no # _item_type.code line # save_ # save__ihm_predicted_contact_restraint.entity_description_2 _item_description.description ; A text description of molecular entity 2. ; # _item.name "_ihm_predicted_contact_restraint.entity_description_2" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code no # _item_type.code line # save_ # save__ihm_predicted_contact_restraint.entity_id_1 _item_description.description ; The entity identifier for the first monomer partner in the predicted contact. This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_predicted_contact_restraint.entity_id_1" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code yes # _item_type.code code # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_1 # _item_linked.child_name "_ihm_predicted_contact_restraint.entity_id_1" _item_linked.parent_name "_entity_poly_seq.entity_id" # save_ # save__ihm_predicted_contact_restraint.entity_id_2 _item_description.description ; The entity identifier for the second monomer partner in the predicted contact. This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_predicted_contact_restraint.entity_id_2" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code yes # _item_type.code code # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_2 # _item_linked.child_name "_ihm_predicted_contact_restraint.entity_id_2" _item_linked.parent_name "_entity_poly_seq.entity_id" # save_ # save__ihm_predicted_contact_restraint.asym_id_1 _item_description.description ; An asym/strand identifier for the first monomer partner in the predicted contact. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_predicted_contact_restraint.asym_id_1" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_predicted_contact_restraint.asym_id_1" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_predicted_contact_restraint.asym_id_2 _item_description.description ; An asym/strand identifier for the second monomer partner in the predicted contact. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_predicted_contact_restraint.asym_id_2" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_predicted_contact_restraint.asym_id_2" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_predicted_contact_restraint.comp_id_1 _item_description.description ; The component identifier for the first monomer partner in the predicted contact. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_predicted_contact_restraint.comp_id_1" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code yes # _item_type.code ucode # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_1 # _item_linked.child_name "_ihm_predicted_contact_restraint.comp_id_1" _item_linked.parent_name "_entity_poly_seq.mon_id" # save_ # save__ihm_predicted_contact_restraint.comp_id_2 _item_description.description ; The component identifier for the second monomer partner in the predicted contact. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_predicted_contact_restraint.comp_id_2" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code yes # _item_type.code ucode # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_2 # _item_linked.child_name "_ihm_predicted_contact_restraint.comp_id_2" _item_linked.parent_name "_entity_poly_seq.mon_id" # save_ # save__ihm_predicted_contact_restraint.seq_id_1 _item_description.description ; The sequence index for the first monomer partner in the predicted contact. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_predicted_contact_restraint.seq_id_1" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_1 # _item_linked.child_name "_ihm_predicted_contact_restraint.seq_id_1" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_predicted_contact_restraint.seq_id_2 _item_description.description ; The sequence index for the second monomer partner in the predicted contact. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_predicted_contact_restraint.seq_id_2" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_2 # _item_linked.child_name "_ihm_predicted_contact_restraint.seq_id_2" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_predicted_contact_restraint.rep_atom_1 _item_description.description ; If _ihm_predicted_contact_restraint.model_granularity is by-residue, then indicate the atom used to represent the first monomer partner in three-dimension. Default is the C-alpha atom. ; # _item.name "_ihm_predicted_contact_restraint.rep_atom_1" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code no # _item_type.code code # _item_default.value CA # loop_ _item_enumeration.value _item_enumeration.detail CA "C-alpha for all residues" CB "C-beta for all residues except Glycine; Default value of C-alpha for Glycine" # save_ # save__ihm_predicted_contact_restraint.rep_atom_2 _item_description.description ; If _ihm_predicted_contact_restraint.model_granularity is by-residue, then indicate the atom used to represent the second monomer partner in three-dimension. Default is the C-alpha atom. ; # _item.name "_ihm_predicted_contact_restraint.rep_atom_2" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code no # _item_type.code code # _item_default.value CA # loop_ _item_enumeration.value _item_enumeration.detail CA "C-alpha for all residues" CB "C-beta for all residues except Glycine; Default value of C-alpha for Glycine" # save_ # save__ihm_predicted_contact_restraint.distance_lower_limit _item_description.description ; The lower limit to the distance threshold applied to this predicted contact restraint in the integrative modeling task. ; # _item.name "_ihm_predicted_contact_restraint.distance_lower_limit" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_predicted_contact_restraint.distance_upper_limit _item_description.description ; The upper limit to the distance threshold applied to this predicted contact restraint in the integrative modeling task. ; # _item.name "_ihm_predicted_contact_restraint.distance_upper_limit" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_predicted_contact_restraint.probability _item_description.description ; The real number that indicates the probability that the predicted distance restraint is correct. This number should fall between 0.0 and 1.0. ; # _item.name "_ihm_predicted_contact_restraint.probability" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code no # _item_type.code float # loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 1.0 1.0 1.0 # save_ # save__ihm_predicted_contact_restraint.restraint_type _item_description.description " The type of distance restraint applied." # _item.name "_ihm_predicted_contact_restraint.restraint_type" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value "lower bound" "upper bound" "lower and upper bound" # save_ # save__ihm_predicted_contact_restraint.model_granularity _item_description.description " The granularity of the predicted contact as applied to the multi-scale model." # _item.name "_ihm_predicted_contact_restraint.model_granularity" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail by-residue "Restraint applied to the specific residue represented by the alpha carbon atom" by-feature "Restraint applied to the closest primitive object with the highest resolution" # save_ # save__ihm_predicted_contact_restraint.dataset_list_id _item_description.description ; Identifier to the predicted contacts dataset. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_predicted_contact_restraint.dataset_list_id" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_predicted_contact_restraint.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save__ihm_predicted_contact_restraint.software_id _item_description.description ; Identifier to the software used to obtain the predicted contacts dataset. This data item is a pointer to the _software.pdbx_ordinal in the SOFTWARE category. ; # _item.name "_ihm_predicted_contact_restraint.software_id" _item.category_id ihm_predicted_contact_restraint _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_predicted_contact_restraint.software_id" _item_linked.parent_name "_software.pdbx_ordinal" # save_ # save_ihm_hydroxyl_radical_fp_restraint _category.description ; Data items in the IHM_HYDROXYL_RADICAL_FP_RESTRAINT category records the restraints derived from hydroxyl radical footprinting experiment. These restraints provide information regarding solvent accessible surface area of residues. ; _category.id ihm_hydroxyl_radical_fp_restraint _category.mandatory_code no # _category_key.name "_ihm_hydroxyl_radical_fp_restraint.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_hydroxyl_radical_fp_restraint.id _ihm_hydroxyl_radical_fp_restraint.entity_id _ihm_hydroxyl_radical_fp_restraint.asym_id _ihm_hydroxyl_radical_fp_restraint.seq_id _ihm_hydroxyl_radical_fp_restraint.comp_id _ihm_hydroxyl_radical_fp_restraint.fp_rate _ihm_hydroxyl_radical_fp_restraint.log_pf _ihm_hydroxyl_radical_fp_restraint.predicted_sasa _ihm_hydroxyl_radical_fp_restraint.dataset_list_id _ihm_hydroxyl_radical_fp_restraint.software_id 1 3 A 17 LYS 5.63 ? 120.2 1 1 2 3 A 33 LYS 4.82 ? 118.1 1 1 3 3 A 38 ILE 0.35 ? 45.6 1 1 4 3 A 42 TYR 2.13 ? 81.4 1 1 5 3 A 48 PHE 3.45 ? 95.3 1 1 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_hydroxyl_radical_fp_restraint # save_ # save__ihm_hydroxyl_radical_fp_restraint.id _item_description.description " A unique identifier for the hydroxyl radical footprinting restraint." # _item.name "_ihm_hydroxyl_radical_fp_restraint.id" _item.category_id ihm_hydroxyl_radical_fp_restraint _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_hydroxyl_radical_fp_restraint.group_id _item_description.description " An identifier to group the hydroxyl radical footprinting restraints." # _item.name "_ihm_hydroxyl_radical_fp_restraint.group_id" _item.category_id ihm_hydroxyl_radical_fp_restraint _item.mandatory_code no # _item_type.code int # save_ # save__ihm_hydroxyl_radical_fp_restraint.entity_description _item_description.description ; A text description of the molecular entity. ; # _item.name "_ihm_hydroxyl_radical_fp_restraint.entity_description" _item.category_id ihm_hydroxyl_radical_fp_restraint _item.mandatory_code no # _item_type.code line # save_ # save__ihm_hydroxyl_radical_fp_restraint.entity_id _item_description.description ; The entity identifier. This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_hydroxyl_radical_fp_restraint.entity_id" _item.category_id ihm_hydroxyl_radical_fp_restraint _item.mandatory_code yes # _item_type.code code # _item_sub_category.id mm_poly_res_label # _item_linked.child_name "_ihm_hydroxyl_radical_fp_restraint.entity_id" _item_linked.parent_name "_entity_poly_seq.entity_id" # save_ # save__ihm_hydroxyl_radical_fp_restraint.asym_id _item_description.description ; An asym/strand identifier. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_hydroxyl_radical_fp_restraint.asym_id" _item.category_id ihm_hydroxyl_radical_fp_restraint _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_hydroxyl_radical_fp_restraint.asym_id" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_hydroxyl_radical_fp_restraint.comp_id _item_description.description ; The component identifier for the residue. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_hydroxyl_radical_fp_restraint.comp_id" _item.category_id ihm_hydroxyl_radical_fp_restraint _item.mandatory_code yes # _item_type.code ucode # _item_sub_category.id mm_poly_res_label # _item_linked.child_name "_ihm_hydroxyl_radical_fp_restraint.comp_id" _item_linked.parent_name "_entity_poly_seq.mon_id" # save_ # save__ihm_hydroxyl_radical_fp_restraint.seq_id _item_description.description ; The sequence index for the residue. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_hydroxyl_radical_fp_restraint.seq_id" _item.category_id ihm_hydroxyl_radical_fp_restraint _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label # _item_linked.child_name "_ihm_hydroxyl_radical_fp_restraint.seq_id" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_hydroxyl_radical_fp_restraint.fp_rate _item_description.description " The footprinting rate." # _item.name "_ihm_hydroxyl_radical_fp_restraint.fp_rate" _item.category_id ihm_hydroxyl_radical_fp_restraint _item.mandatory_code no # _item_type.code float # _item_units.code reciprocal_seconds # save_ # save__ihm_hydroxyl_radical_fp_restraint.fp_rate_error _item_description.description " The footprinting rate error." # _item.name "_ihm_hydroxyl_radical_fp_restraint.fp_rate_error" _item.category_id ihm_hydroxyl_radical_fp_restraint _item.mandatory_code no # _item_type.code float # _item_units.code reciprocal_seconds # save_ # save__ihm_hydroxyl_radical_fp_restraint.log_pf _item_description.description " Log (base 10) protection factor." # _item.name "_ihm_hydroxyl_radical_fp_restraint.log_pf" _item.category_id ihm_hydroxyl_radical_fp_restraint _item.mandatory_code no # _item_type.code float # save_ # save__ihm_hydroxyl_radical_fp_restraint.log_pf_error _item_description.description " Error of Log (base 10) protection factor." # _item.name "_ihm_hydroxyl_radical_fp_restraint.log_pf_error" _item.category_id ihm_hydroxyl_radical_fp_restraint _item.mandatory_code no # _item_type.code float # save_ # save__ihm_hydroxyl_radical_fp_restraint.predicted_sasa _item_description.description " The predicted solvent accessible surface area." # _item.name "_ihm_hydroxyl_radical_fp_restraint.predicted_sasa" _item.category_id ihm_hydroxyl_radical_fp_restraint _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms_squared # save_ # save__ihm_hydroxyl_radical_fp_restraint.dataset_list_id _item_description.description ; Identifier to the hydroxyl radical footprinting dataset. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_hydroxyl_radical_fp_restraint.dataset_list_id" _item.category_id ihm_hydroxyl_radical_fp_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_hydroxyl_radical_fp_restraint.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save__ihm_hydroxyl_radical_fp_restraint.software_id _item_description.description ; Identifier to the software used to obtain the restraint. This data item is a pointer to the _software.pdbx_ordinal in the SOFTWARE category. ; # _item.name "_ihm_hydroxyl_radical_fp_restraint.software_id" _item.category_id ihm_hydroxyl_radical_fp_restraint _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_hydroxyl_radical_fp_restraint.software_id" _item_linked.parent_name "_software.pdbx_ordinal" # save_ # save_ihm_chemical_component_descriptor _category.description ; Data items in the IHM_CHEMICAL_COMPONENT_DESCRIPTOR category records the details of the chemical descriptors of various non-polymeric chemical components (fluorescent probes, crosslinking agents etc.) used in the experiments. ; _category.id ihm_chemical_component_descriptor _category.mandatory_code no # _category_key.name "_ihm_chemical_component_descriptor.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_chemical_component_descriptor.id _ihm_chemical_component_descriptor.chemical_name _ihm_chemical_component_descriptor.auth_name _ihm_chemical_component_descriptor.smiles _ihm_chemical_component_descriptor.inchi _ihm_chemical_component_descriptor.inchi_key 1 "1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride" "EDC" "CCN=C=NCCCN(C)C" "1S/C8H17N3/c1-4-9-8-10-6-5-7-11(2)3/h4-7H2,1-3H3" "LMDZBCPBFSXMTL-UHFFFAOYSA-N" 2 "disuccinimidyl suberate" "DSS" "C1CC(=O)N(C1=O)OC(=O)CCCCCCC(=O)ON2C(=O)CCC2=O" "1S/C16H20N2O8/c19-11-7-8-12(20)17(11)25-15(23)5-3-1-2-4-6-16(24)26-18-13(21)9-10-14(18)22/h1-10H2" "ZWIBGKZDAWNIFC-UHFFFAOYSA-N" # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_chemical_component_descriptor # save_ # save__ihm_chemical_component_descriptor.id _item_description.description " An identifier for the chemical descriptor." # _item.name "_ihm_chemical_component_descriptor.id" _item.category_id ihm_chemical_component_descriptor _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_chemical_component_descriptor.chemical_name _item_description.description " The chemical name of the component." # _item.name "_ihm_chemical_component_descriptor.chemical_name" _item.category_id ihm_chemical_component_descriptor _item.mandatory_code no # _item_type.code line # save_ # save__ihm_chemical_component_descriptor.common_name _item_description.description " The common name of the component." # _item.name "_ihm_chemical_component_descriptor.common_name" _item.category_id ihm_chemical_component_descriptor _item.mandatory_code no # _item_type.code line # save_ # save__ihm_chemical_component_descriptor.auth_name _item_description.description " The author-provided name of the component." # _item.name "_ihm_chemical_component_descriptor.auth_name" _item.category_id ihm_chemical_component_descriptor _item.mandatory_code yes # _item_type.code line # save_ # save__ihm_chemical_component_descriptor.smiles _item_description.description " The smile string of the component." # _item.name "_ihm_chemical_component_descriptor.smiles" _item.category_id ihm_chemical_component_descriptor _item.mandatory_code no # _item_type.code line # save_ # save__ihm_chemical_component_descriptor.smiles_canonical _item_description.description " The canonical smile string of the component." # _item.name "_ihm_chemical_component_descriptor.smiles_canonical" _item.category_id ihm_chemical_component_descriptor _item.mandatory_code no # _item_type.code line # save_ # save__ihm_chemical_component_descriptor.inchi _item_description.description " The IUPAC INCHI descriptor of the component." # _item.name "_ihm_chemical_component_descriptor.inchi" _item.category_id ihm_chemical_component_descriptor _item.mandatory_code no # _item_type.code line # save_ # save__ihm_chemical_component_descriptor.inchi_key _item_description.description " The hashed INCHI key of the component." # _item.name "_ihm_chemical_component_descriptor.inchi_key" _item.category_id ihm_chemical_component_descriptor _item.mandatory_code no # _item_type.code line # save_ # save__ihm_chemical_component_descriptor.details _item_description.description " Additional details regarding the chemical component." # _item.name "_ihm_chemical_component_descriptor.details" _item.category_id ihm_chemical_component_descriptor _item.mandatory_code no # _item_type.code text # save_ # save_ihm_probe_list _category.description ; Data items in the IHM_PROBE_LIST category records the list of probes used in the experiment. ; _category.id ihm_probe_list _category.mandatory_code no # _category_key.name "_ihm_probe_list.probe_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_probe_list.probe_id _ihm_probe_list.probe_name _ihm_probe_list.probe_origin _ihm_probe_list.probe_link_type _ihm_probe_list.probe_chem_comp_descriptor_id _ihm_probe_list.reactive_probe_flag _ihm_probe_list.reactive_probe_name _ihm_probe_list.reactive_probe_chem_comp_descriptor_id 1 MTSL extrinsic covalent 1 ? ? ? # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_probe_list # save_ # save__ihm_probe_list.probe_id _item_description.description " A unique identifier for the category." # _item.name "_ihm_probe_list.probe_id" _item.category_id ihm_probe_list _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_probe_list.probe_name _item_description.description " Author provided name for the probe." # _item.name "_ihm_probe_list.probe_name" _item.category_id ihm_probe_list _item.mandatory_code yes # _item_type.code line # save_ # save__ihm_probe_list.reactive_probe_flag _item_description.description " Indicate whether the probe has a reactive form." # _item.name "_ihm_probe_list.reactive_probe_flag" _item.category_id ihm_probe_list _item.mandatory_code no # _item_type.code ucode # loop_ _item_enumeration.value yes no # save_ # save__ihm_probe_list.reactive_probe_name _item_description.description " Author provided name for the reactive_probe, if applicable." # _item.name "_ihm_probe_list.reactive_probe_name" _item.category_id ihm_probe_list _item.mandatory_code no # _item_type.code line # save_ # save__ihm_probe_list.probe_origin _item_description.description " The origin of the probe." # _item.name "_ihm_probe_list.probe_origin" _item.category_id ihm_probe_list _item.mandatory_code yes # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail intrinsic "a probe which is an instrinsic part of the biomolecule; eg: Tryptophan or Flavins or metals in EPR" extrinsic "a probe that has been synthetically introduced for carrying out the experiment; eg: organic probe Alexa 488 or MANT-ATP" # save_ # save__ihm_probe_list.probe_link_type _item_description.description " The type of link between the probe and the biomolecule." # _item.name "_ihm_probe_list.probe_link_type" _item.category_id ihm_probe_list _item.mandatory_code yes # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail covalent "a probe which is covalently linked to a particular residue in the polymeric marcomolecule; eg: Tryptophan in proteins or Alexa 488" ligand "a ligand probe that is not covalently linked to the macromolecule; eg: Flavins, MANT-ATP" # save_ # save__ihm_probe_list.probe_chem_comp_descriptor_id _item_description.description ; The identifier for the chemical descriptor of the probe. This data item is a pointer to _ihm_chemical_component_descriptor.id in the IHM_CHEMICAL_COMPONENT_DESCRIPTOR category. ; # _item.name "_ihm_probe_list.probe_chem_comp_descriptor_id" _item.category_id ihm_probe_list _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_probe_list.probe_chem_comp_descriptor_id" _item_linked.parent_name "_ihm_chemical_component_descriptor.id" # save_ # save__ihm_probe_list.reactive_probe_chem_comp_descriptor_id _item_description.description ; The identifier for the chemical descriptor of the reactive probe. This data item is a pointer to _ihm_chemical_component_descriptor.id in the IHM_CHEMICAL_COMPONENT_DESCRIPTOR category. ; # _item.name "_ihm_probe_list.reactive_probe_chem_comp_descriptor_id" _item.category_id ihm_probe_list _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_probe_list.reactive_probe_chem_comp_descriptor_id" _item_linked.parent_name "_ihm_chemical_component_descriptor.id" # save_ # save_ihm_poly_probe_position _category.description ; Data items in the IHM_POLY_PROBE_POSITION category identifies specific residue positions in the polymeric entity where probes are covalently attached. ; _category.id ihm_poly_probe_position _category.mandatory_code no # _category_key.name "_ihm_poly_probe_position.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_poly_probe_position.id _ihm_poly_probe_position.entity_id _ihm_poly_probe_position.entity_description _ihm_poly_probe_position.comp_id _ihm_poly_probe_position.seq_id _ihm_poly_probe_position.mutation_flag _ihm_poly_probe_position.modification_flag _ihm_poly_probe_position.mut_res_chem_comp_id _ihm_poly_probe_position.mod_res_chem_comp_descriptor_id _ihm_poly_probe_position.description 1 1 ? LYS 340 yes no CYS ? ? 2 1 ? VAL 354 yes no CYS ? ? 3 1 ? LEU 372 yes no CYS ? ? # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_poly_probe_position # save_ # save__ihm_poly_probe_position.id _item_description.description " A unique identifier for the category." # _item.name "_ihm_poly_probe_position.id" _item.category_id ihm_poly_probe_position _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_poly_probe_position.entity_id _item_description.description ; A unique identifier for the entity where the probe is attached. This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_poly_probe_position.entity_id" _item.category_id ihm_poly_probe_position _item.mandatory_code yes # _item_type.code code # _item_sub_category.id mm_poly_res_label # _item_linked.child_name "_ihm_poly_probe_position.entity_id" _item_linked.parent_name "_entity_poly_seq.entity_id" # save_ # save__ihm_poly_probe_position.entity_description _item_description.description " Description of the entity." # _item.name "_ihm_poly_probe_position.entity_description" _item.category_id ihm_poly_probe_position _item.mandatory_code no # _item_type.code line # save_ # save__ihm_poly_probe_position.seq_id _item_description.description ; The sequence index of the residue in the entity where the probe is attached. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_poly_probe_position.seq_id" _item.category_id ihm_poly_probe_position _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label # _item_linked.child_name "_ihm_poly_probe_position.seq_id" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_poly_probe_position.comp_id _item_description.description ; The component identifier of the residue in the entity where the probe is attached. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_poly_probe_position.comp_id" _item.category_id ihm_poly_probe_position _item.mandatory_code yes # _item_type.code ucode # _item_sub_category.id mm_poly_res_label # _item_linked.child_name "_ihm_poly_probe_position.comp_id" _item_linked.parent_name "_entity_poly_seq.mon_id" # save_ # save__ihm_poly_probe_position.mutation_flag _item_description.description " A flag to indicate whether the residue has an engineered mutation or not." # _item.name "_ihm_poly_probe_position.mutation_flag" _item.category_id ihm_poly_probe_position _item.mandatory_code yes # _item_type.code ucode # loop_ _item_enumeration.value yes no # save_ # save__ihm_poly_probe_position.mut_res_chem_comp_id _item_description.description ; The chemical component identifier of the mutated residue, if applicable. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; # _item.name "_ihm_poly_probe_position.mut_res_chem_comp_id" _item.category_id ihm_poly_probe_position _item.mandatory_code no # _item_type.code ucode # _item_linked.child_name "_ihm_poly_probe_position.mut_res_chem_comp_id" _item_linked.parent_name "_chem_comp.id" # loop_ _item_examples.case CYS TRP # save_ # save__ihm_poly_probe_position.modification_flag _item_description.description " A flag to indicate whether the residue is chemically modified or not." # _item.name "_ihm_poly_probe_position.modification_flag" _item.category_id ihm_poly_probe_position _item.mandatory_code yes # _item_type.code ucode # loop_ _item_enumeration.value yes no # save_ # save__ihm_poly_probe_position.mod_res_chem_comp_descriptor_id _item_description.description ; An identifier to the chemical descriptor of the modified residue, if applicable. This data item is a pointer to _ihm_chemical_component_descriptor.id in the IHM_CHEMICAL_COMPONENT_DESCRIPTOR category. ; # _item.name "_ihm_poly_probe_position.mod_res_chem_comp_descriptor_id" _item.category_id ihm_poly_probe_position _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_poly_probe_position.mod_res_chem_comp_descriptor_id" _item_linked.parent_name "_ihm_chemical_component_descriptor.id" # save_ # save__ihm_poly_probe_position.description _item_description.description " An author provided description for the residue position in the polymer." # _item.name "_ihm_poly_probe_position.description" _item.category_id ihm_poly_probe_position _item.mandatory_code no # _item_type.code line # save_ # save_ihm_poly_probe_conjugate _category.description ; Data items in the IHM_POLY_PROBE_CONJUGATE category records the details of the probes that are covalenty attached to residues in the polymeric entities. ; _category.id ihm_poly_probe_conjugate _category.mandatory_code no # _category_key.name "_ihm_poly_probe_conjugate.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_poly_probe_conjugate.id _ihm_poly_probe_conjugate.probe_id _ihm_poly_probe_conjugate.position_id _ihm_poly_probe_conjugate.chem_comp_descriptor_id _ihm_poly_probe_conjugate.ambiguous_stoichiometry_flag _ihm_poly_probe_conjugate.probe_stoichiometry _ihm_poly_probe_conjugate.details _ihm_poly_probe_conjugate.dataset_list_id 1 1 1 ? ? ? ? 2 2 1 2 ? ? ? ? 2 3 1 3 ? ? ? ? 2 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_poly_probe_conjugate # save_ # save__ihm_poly_probe_conjugate.id _item_description.description " A unique identifier for the category." # _item.name "_ihm_poly_probe_conjugate.id" _item.category_id ihm_poly_probe_conjugate _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_poly_probe_conjugate.probe_id _item_description.description ; An identifier for the probe. This data item is a pointer to _ihm_probe_list.probe_id in the IHM_PROBE_LIST category. ; # _item.name "_ihm_poly_probe_conjugate.probe_id" _item.category_id ihm_poly_probe_conjugate _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_poly_probe_conjugate.probe_id" _item_linked.parent_name "_ihm_probe_list.probe_id" # save_ # save__ihm_poly_probe_conjugate.position_id _item_description.description ; An identifier for the position in the polymeric entity where the probe is attached. This data item is a pointer to _ihm_poly_probe_position.id in the IHM_POLY_PROBE_POSITION category. ; # _item.name "_ihm_poly_probe_conjugate.position_id" _item.category_id ihm_poly_probe_conjugate _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_poly_probe_conjugate.position_id" _item_linked.parent_name "_ihm_poly_probe_position.id" # save_ # save__ihm_poly_probe_conjugate.chem_comp_descriptor_id _item_description.description ; The chemical descriptor of the polymeric residue conjugate with the probe. This data item is a pointer to _ihm_chemical_component_descriptor.id in the IHM_CHEMICAL_COMPONENT_DESCRIPTOR category. ; # _item.name "_ihm_poly_probe_conjugate.chem_comp_descriptor_id" _item.category_id ihm_poly_probe_conjugate _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_poly_probe_conjugate.chem_comp_descriptor_id" _item_linked.parent_name "_ihm_chemical_component_descriptor.id" # save_ # save__ihm_poly_probe_conjugate.ambiguous_stoichiometry_flag _item_description.description " Indicate whether there is ambiguity regarding the stoichiometry of the labeled site." # _item.name "_ihm_poly_probe_conjugate.ambiguous_stoichiometry_flag" _item.category_id ihm_poly_probe_conjugate _item.mandatory_code no # _item_type.code ucode # loop_ _item_enumeration.value yes no # save_ # save__ihm_poly_probe_conjugate.probe_stoichiometry _item_description.description " The stoichiometry of the probe labeling site, if known." # _item.name "_ihm_poly_probe_conjugate.probe_stoichiometry" _item.category_id ihm_poly_probe_conjugate _item.mandatory_code no # _item_type.code float # save_ # save__ihm_poly_probe_conjugate.details _item_description.description " Additional details regarding the conjugate." # _item.name "_ihm_poly_probe_conjugate.details" _item.category_id ihm_poly_probe_conjugate _item.mandatory_code no # _item_type.code text # save_ # save__ihm_poly_probe_conjugate.dataset_list_id _item_description.description ; An identifier for the experimental dataset corresponding to the polymer-probe conjugate. This data item is a pointer to _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_poly_probe_conjugate.dataset_list_id" _item.category_id ihm_poly_probe_conjugate _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_poly_probe_conjugate.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save_ihm_ligand_probe _category.description ; Data items in the IHM_LIGAND_PROBE category identifies non-polymeric entities (ligands) that are used as probes. ; _category.id ihm_ligand_probe _category.mandatory_code no # _category_key.name "_ihm_ligand_probe.probe_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_ligand_probe.probe_id _ihm_ligand_probe.entity_id _ihm_ligand_probe.dataset_list_id _ihm_ligand_probe.details 1 3 1 ? 2 4 1 ? # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_ligand_probe # save_ # save__ihm_ligand_probe.probe_id _item_description.description ; An identifier for the probe. This data item is a pointer to _ihm_probe_list.probe_id in the IHM_PROBE_LIST category. ; # _item.name "_ihm_ligand_probe.probe_id" _item.category_id ihm_ligand_probe _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_ligand_probe.probe_id" _item_linked.parent_name "_ihm_probe_list.probe_id" # save_ # save__ihm_ligand_probe.entity_id _item_description.description ; The entity id of the ligand. This data item is a pointer to _entity.id in the ENTITY category. ; # _item.name "_ihm_ligand_probe.entity_id" _item.category_id ihm_ligand_probe _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_ligand_probe.entity_id" _item_linked.parent_name "_entity.id" # save_ # save__ihm_ligand_probe.details _item_description.description " Additional details regarding the ligand probe." # _item.name "_ihm_ligand_probe.details" _item.category_id ihm_ligand_probe _item.mandatory_code no # _item_type.code text # save_ # save__ihm_ligand_probe.dataset_list_id _item_description.description ; An identifier for the experimental dataset corresponding to the ligand probe. This data item is a pointer to _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_ligand_probe.dataset_list_id" _item.category_id ihm_ligand_probe _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_ligand_probe.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save_ihm_epr_restraint _category.description ; Data items in the IHM_EPR_RESTRAINT category records the details of the EPR data used as restraints in the IHM modeling. ; _category.id ihm_epr_restraint _category.mandatory_code no # _category_key.name "_ihm_epr_restraint.ordinal_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; _ihm_epr_restraint.ordinal_id 1 _ihm_epr_restraint.dataset_list_id 8 _ihm_epr_restraint.model_id 1 _ihm_epr_restraint.fitting_particle_type 'Unpaired electron of the label' _ihm_epr_restraint.fitting_method 'Spin label rotamer refinement using DEER/PELDOR data' _ihm_epr_restraint.fitting_method_citation_id 3 _ihm_epr_restraint.fitting_state 'Single' _ihm_epr_restraint.fitting_software_id 1 _ihm_epr_restraint.chi_value 0.06 _ihm_epr_restraint.details . ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_epr_restraint # save_ # save__ihm_epr_restraint.ordinal_id _item_description.description " A unique identifier for the EPR restraint description." # _item.name "_ihm_epr_restraint.ordinal_id" _item.category_id ihm_epr_restraint _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_epr_restraint.dataset_list_id _item_description.description ; Identifier to the EPR data used. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_epr_restraint.dataset_list_id" _item.category_id ihm_epr_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_epr_restraint.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save__ihm_epr_restraint.model_id _item_description.description ; The model number corresponding to the EPR fitting result presented. This data item is a pointer to _ihm_model_list.model_id in the IHM_MODEL_LIST category. ; # _item.name "_ihm_epr_restraint.model_id" _item.category_id ihm_epr_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_epr_restraint.model_id" _item_linked.parent_name "_ihm_model_list.model_id" # save_ # save__ihm_epr_restraint.fitting_particle_type _item_description.description " The type of particle fit to the EPR data." # _item.name "_ihm_epr_restraint.fitting_particle_type" _item.category_id ihm_epr_restraint _item.mandatory_code no # _item_type.code line # _item_examples.case "Unpaired electrons of the probe" # save_ # save__ihm_epr_restraint.fitting_method _item_description.description " The method used for fitting the model to the EPR data." # _item.name "_ihm_epr_restraint.fitting_method" _item.category_id ihm_epr_restraint _item.mandatory_code no # _item_type.code line # _item_examples.case "Spin label rotamer refinement using DEER/PELDOR data" # save_ # save__ihm_epr_restraint.fitting_method_citation_id _item_description.description ; Identifier pointing to the citation for the fitting method. This data item is a pointer to _citation.id in the CITATION category. ; # _item.name "_ihm_epr_restraint.fitting_method_citation_id" _item.category_id ihm_epr_restraint _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_ihm_epr_restraint.fitting_method_citation_id" _item_linked.parent_name "_citation.id" # save_ # save__ihm_epr_restraint.fitting_state _item_description.description " An indicator to single or multiple state fitting." # _item.name "_ihm_epr_restraint.fitting_state" _item.category_id ihm_epr_restraint _item.mandatory_code no # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail Single "Single-state fitting" Multiple "Multi-state fitting" # save_ # save__ihm_epr_restraint.fitting_software_id _item_description.description ; Identifier pointing to the software used for fitting. This data item is a pointer to _software.pdbx_ordinal in the SOFTWARE category. ; # _item.name "_ihm_epr_restraint.fitting_software_id" _item.category_id ihm_epr_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_epr_restraint.fitting_software_id" _item_linked.parent_name "_software.pdbx_ordinal" # save_ # save__ihm_epr_restraint.chi_value _item_description.description " The chi value resulting from fitting the model to the EPR data." # _item.name "_ihm_epr_restraint.chi_value" _item.category_id ihm_epr_restraint _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_epr_restraint.details _item_description.description " Additional details regarding the EPR restraint used." # _item.name "_ihm_epr_restraint.details" _item.category_id ihm_epr_restraint _item.mandatory_code no # _item_type.code text # save_ # save_ihm_cross_link_list _category.description ; Data items in the IHM_CROSS_LINK_LIST category records the list of spatial restraints derived from chemical crosslinking experiment. ; _category.id ihm_cross_link_list _category.mandatory_code no # _category_key.name "_ihm_cross_link_list.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_cross_link_list.id _ihm_cross_link_list.group_id _ihm_cross_link_list.entity_description_1 _ihm_cross_link_list.entity_id_1 _ihm_cross_link_list.seq_id_1 _ihm_cross_link_list.comp_id_1 _ihm_cross_link_list.entity_description_2 _ihm_cross_link_list.entity_id_2 _ihm_cross_link_list.seq_id_2 _ihm_cross_link_list.comp_id_2 _ihm_cross_link_list.linker_type _ihm_cross_link_list.dataset_list_id 1 1 Nup120 3 17 LYS Nup120 3 421 GLU EDC 1 2 2 Nup120 3 206 LYS Nup120 3 219 ASP EDC 1 3 3 Nup120 3 38 LYS Nup120 3 429 GLU EDC 1 4 4 Nup120 3 400 LYS Nup120 3 440 GLU EDC 1 5 4 Nup120 3 400 LYS Nup120 3 441 GLU EDC 1 6 5 Nup120 3 400 LYS Nup120 3 523 ASP EDC 1 7 6 Nup120 3 735 LYS Nup120 3 403 ASP EDC 1 8 6 Nup120 3 735 LYS Nup120 3 405 GLU EDC 1 9 7 Nup120 3 865 LYS Nup120 3 894 GLU EDC 1 10 7 Nup120 3 865 LYS Nup120 3 898 ASP EDC 1 11 8 Nup133 4 103 LYS Nup133 4 130 ASP EDC 1 12 8 Nup133 4 103 LYS Nup133 4 131 GLU EDC 1 13 9 Nup120 3 17 LYS Nup120 3 412 LYS DSS 2 14 10 Nup120 3 17 LYS Nup120 3 735 LYS DSS 2 15 11 Nup120 3 206 LYS Nup120 3 217 LYS DSS 2 16 12 Nup120 3 384 LYS Nup120 3 362 LYS DSS 2 17 13 Nup120 3 400 LYS Nup120 3 530 LYS DSS 2 18 14 Nup120 3 400 LYS Nup120 3 531 LYS DSS 2 19 15 Nup120 3 400 LYS Nup120 3 735 LYS DSS 2 20 16 Nup120 3 735 LYS Nup120 3 412 LYS DSS 2 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_cross_link_list # save_ # save__ihm_cross_link_list.id _item_description.description " A unique identifier for the cross link restraint." # _item.name "_ihm_cross_link_list.id" _item.category_id ihm_cross_link_list _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_cross_link_list.group_id _item_description.description ; An identifier for a set of ambiguous crosslink restraints. Handles experimental uncertainties in the identities of crosslinked residues. ; # _item.name "_ihm_cross_link_list.group_id" _item.category_id ihm_cross_link_list _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_cross_link_list.entity_description_1 _item_description.description ; A text description of molecular entity 1. ; # _item.name "_ihm_cross_link_list.entity_description_1" _item.category_id ihm_cross_link_list _item.mandatory_code no # _item_type.code line # save_ # save__ihm_cross_link_list.entity_description_2 _item_description.description ; A text description of molecular entity 2. ; # _item.name "_ihm_cross_link_list.entity_description_2" _item.category_id ihm_cross_link_list _item.mandatory_code no # _item_type.code line # save_ # save__ihm_cross_link_list.entity_id_1 _item_description.description ; The entity identifier for the first monomer partner in the cross link This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_cross_link_list.entity_id_1" _item.category_id ihm_cross_link_list _item.mandatory_code yes # _item_type.code code # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_1 # _item_linked.child_name "_ihm_cross_link_list.entity_id_1" _item_linked.parent_name "_entity_poly_seq.entity_id" # save_ # save__ihm_cross_link_list.entity_id_2 _item_description.description ; The entity identifier for the second monomer partner in the cross link This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_cross_link_list.entity_id_2" _item.category_id ihm_cross_link_list _item.mandatory_code yes # _item_type.code code # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_2 # _item_linked.child_name "_ihm_cross_link_list.entity_id_2" _item_linked.parent_name "_entity_poly_seq.entity_id" # save_ # save__ihm_cross_link_list.comp_id_1 _item_description.description ; The component identifier for the first monomer partner in the cross link. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_cross_link_list.comp_id_1" _item.category_id ihm_cross_link_list _item.mandatory_code yes # _item_type.code ucode # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_1 # _item_linked.child_name "_ihm_cross_link_list.comp_id_1" _item_linked.parent_name "_entity_poly_seq.mon_id" # save_ # save__ihm_cross_link_list.comp_id_2 _item_description.description ; The component identifier for the second monomer partner in the cross link. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_cross_link_list.comp_id_2" _item.category_id ihm_cross_link_list _item.mandatory_code yes # _item_type.code ucode # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_2 # _item_linked.child_name "_ihm_cross_link_list.comp_id_2" _item_linked.parent_name "_entity_poly_seq.mon_id" # save_ # save__ihm_cross_link_list.seq_id_1 _item_description.description ; The sequence index for the first monomer partner in the cross link. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_cross_link_list.seq_id_1" _item.category_id ihm_cross_link_list _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_1 # _item_linked.child_name "_ihm_cross_link_list.seq_id_1" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_cross_link_list.seq_id_2 _item_description.description ; The sequence index for the second monomer partner in the cross link. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_cross_link_list.seq_id_2" _item.category_id ihm_cross_link_list _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_2 # _item_linked.child_name "_ihm_cross_link_list.seq_id_2" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_cross_link_list.linker_type _item_description.description " The type of crosslinker used." # _item.name "_ihm_cross_link_list.linker_type" _item.category_id ihm_cross_link_list _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail EDC "1-ethyl-(dimethylaminopropyl) carbodiimide hydrochloride (EDC) crosslinker" DSS "disuccinimidyl suberate (DSS) crosslinker" EGS "ethylene glycol bis(succinimidyl succinate) crosslinker" BS3 "bis(sulfosuccinimidyl) suberate crosslinker" BS2G "Bis-(sulfosuccinimidyl) glutarate crosslinker" DST "disuccinimidyl tartrate crosslinker" sulfo-SDA "sulfosuccinimidyl 4,4'-azipentanoate, heterobifunctional crosslinker" sulfo-SMCC "sulfosuccinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate crosslinker" DSSO "disuccinimidyl sulfoxide (DSSO) crosslinker" DSG "disuccinimidyl glutarate crosslinker" BSP "Bis(succinimidyl) penta(ethylene glycol) crosslinker" BMSO "bismaleimide sulfoxide crosslinker" DHSO "dihydrazide sulfoxide crosslinker" CYS "Cysteine crosslinker" SDA "succinimidyl 4,4'-azipentanoate" DSA "DiSuccinimidyl Adipate" BrdU "5-bromo-2'-deoxyuridine" LCSDA "succinimidyl 6-(4,4'-azipentanamido)hexanoate" CDI "1,1'-carbonyldiimidazole" ADH "(1Z,6Z)-Hexanedihydrazonic acid" L-Photo-Leucine "L-Photo-Leucine crosslinker" KArGO "arginine-lysine hetero-bifunctional aromatic glyoxal crosslinker" BrEtY "O-(2-bromoethyl)-tyrosine (non-canonical amino acid)" DSBU "Disuccinimidyl dibutyric urea" DSPP "Disuccinimidyl phenyl phosphonic acid or PhoX" TBDSPP "tert-butyl disuccinimidyl phenyl phosphonate or tBu-PhoX" Other "Other type of crosslinker" # save_ # save__ihm_cross_link_list.linker_chem_comp_descriptor_id _item_description.description ; Pointer to the chemical description of the linker. Data item points to _ihm_chemical_component_descriptor.id in the IHM_CHEMICAL_COMPONENT_DESCRIPTOR category. ; # _item.name "_ihm_cross_link_list.linker_chem_comp_descriptor_id" _item.category_id ihm_cross_link_list _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_cross_link_list.linker_chem_comp_descriptor_id" _item_linked.parent_name "_ihm_chemical_component_descriptor.id" # save_ # save__ihm_cross_link_list.dataset_list_id _item_description.description ; Identifier to the crosslinking dataset. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_cross_link_list.dataset_list_id" _item.category_id ihm_cross_link_list _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_cross_link_list.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save__ihm_cross_link_list.details _item_description.description " Additional details regarding the cross link or the cross linking agent." # _item.name "_ihm_cross_link_list.details" _item.category_id ihm_cross_link_list _item.mandatory_code no # _item_type.code text # save_ # save_ihm_cross_link_restraint _category.description ; Data items in the IHM_CROSS_LINK_RESTRAINT category enumerates the implementation details of the chemical crosslinking restraints in the integrative modeling. This category holds the details of how the experimentally derived crosslinks are applied in the modeling. ; _category.id ihm_cross_link_restraint _category.mandatory_code no # _category_key.name "_ihm_cross_link_restraint.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_cross_link_restraint.id _ihm_cross_link_restraint.group_id _ihm_cross_link_restraint.entity_id_1 _ihm_cross_link_restraint.asym_id_1 _ihm_cross_link_restraint.seq_id_1 _ihm_cross_link_restraint.comp_id_1 _ihm_cross_link_restraint.entity_id_2 _ihm_cross_link_restraint.asym_id_2 _ihm_cross_link_restraint.seq_id_2 _ihm_cross_link_restraint.comp_id_2 _ihm_cross_link_restraint.conditional_crosslink_flag _ihm_cross_link_restraint.model_granularity _ihm_cross_link_restraint.distance_threshold _ihm_cross_link_restraint.restraint_type _ihm_cross_link_restraint.psi _ihm_cross_link_restraint.sigma_1 _ihm_cross_link_restraint.sigma_2 1 1 3 C 17 LYS 3 C 421 GLU ALL by-residue 25.0 'upper bound' 0.05 0.01 0.01 2 2 3 C 206 LYS 3 C 219 ASP ALL by-residue 25.0 'upper bound' 0.05 0.01 0.01 3 3 3 C 38 LYS 3 C 429 GLU ALL by-residue 25.0 'upper bound' 0.05 0.01 0.01 4 4 3 C 400 LYS 3 C 440 GLU ALL by-residue 25.0 'upper bound' 0.05 0.01 0.01 5 5 3 C 400 LYS 3 C 441 GLU ALL by-residue 25.0 'upper bound' 0.05 0.01 0.01 6 6 3 C 400 LYS 3 C 523 ASP ALL by-residue 25.0 'upper bound' 0.05 0.01 0.01 7 7 3 C 735 LYS 3 C 403 ASP ALL by-residue 25.0 'upper bound' 0.05 0.01 0.01 8 8 3 C 735 LYS 3 C 405 GLU ALL by-residue 25.0 'upper bound' 0.05 0.01 0.01 9 9 3 C 865 LYS 3 C 894 GLU ALL by-residue 25.0 'upper bound' 0.05 0.01 0.01 10 10 3 C 865 LYS 3 C 898 ASP ALL by-residue 25.0 'upper bound' 0.05 0.01 0.01 11 11 4 D 103 LYS 4 D 130 ASP ALL by-residue 25.0 'upper bound' 0.05 0.01 0.01 12 12 4 D 103 LYS 4 D 131 GLU ALL by-residue 25.0 'upper bound' 0.05 0.01 0.01 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_cross_link_restraint # save_ # save__ihm_cross_link_restraint.id _item_description.description " A unique identifier for the cross link record." # _item.name "_ihm_cross_link_restraint.id" _item.category_id ihm_cross_link_restraint _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_cross_link_restraint.group_id _item_description.description ; An identifier for a set of ambiguous cross-links. Handles implementation uncertainties related to multiple copies of subunit. This data item is a pointer to _ihm_cross_link_list.id in the IHM_CROSS_LINK_LIST category. ; # _item.name "_ihm_cross_link_restraint.group_id" _item.category_id ihm_cross_link_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_cross_link_restraint.group_id" _item_linked.parent_name "_ihm_cross_link_list.id" # save_ # save__ihm_cross_link_restraint.entity_id_1 _item_description.description ; The entity identifier for the first monomer partner in the cross link This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category and the _ihm_cross_link_restraint.entity_id_1 in the IHM_CROSS_LINK_RESTRAINT category. ; # _item.name "_ihm_cross_link_restraint.entity_id_1" _item.category_id ihm_cross_link_restraint _item.mandatory_code yes # _item_type.code code # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_1 # _item_linked.child_name "_ihm_cross_link_restraint.entity_id_1" _item_linked.parent_name "_entity_poly_seq.entity_id" # save_ # save__ihm_cross_link_restraint.entity_id_2 _item_description.description ; The entity identifier for the second monomer partner in the cross link This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category and the _ihm_cross_link_restraint.entity_id_2 in the IHM_CROSS_LINK_RESTRAINT category. ; # _item.name "_ihm_cross_link_restraint.entity_id_2" _item.category_id ihm_cross_link_restraint _item.mandatory_code yes # _item_type.code code # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_2 # _item_linked.child_name "_ihm_cross_link_restraint.entity_id_2" _item_linked.parent_name "_entity_poly_seq.entity_id" # save_ # save__ihm_cross_link_restraint.asym_id_1 _item_description.description ; An asym/strand identifier for the first monomer partner in the cross-link. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_cross_link_restraint.asym_id_1" _item.category_id ihm_cross_link_restraint _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_cross_link_restraint.asym_id_1" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_cross_link_restraint.asym_id_2 _item_description.description ; An asym/strand identifier for the second monomer partner in the cross-link. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_cross_link_restraint.asym_id_2" _item.category_id ihm_cross_link_restraint _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_cross_link_restraint.asym_id_2" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_cross_link_restraint.comp_id_1 _item_description.description ; The component identifier for the first monomer partner in the cross link. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category and the _ihm_cross_link_restraint.comp_id_1 in the IHM_CROSS_LINK_RESTRAINT category. ; # _item.name "_ihm_cross_link_restraint.comp_id_1" _item.category_id ihm_cross_link_restraint _item.mandatory_code yes # _item_type.code ucode # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_1 # _item_linked.child_name "_ihm_cross_link_restraint.comp_id_1" _item_linked.parent_name "_entity_poly_seq.mon_id" # save_ # save__ihm_cross_link_restraint.comp_id_2 _item_description.description ; The component identifier for the second monomer partner in the cross link. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category and the _ihm_cross_link_restraint.comp_id_2 in the IHM_CROSS_LINK_RESTRAINT category. ; # _item.name "_ihm_cross_link_restraint.comp_id_2" _item.category_id ihm_cross_link_restraint _item.mandatory_code yes # _item_type.code ucode # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_2 # _item_linked.child_name "_ihm_cross_link_restraint.comp_id_2" _item_linked.parent_name "_entity_poly_seq.mon_id" # save_ # save__ihm_cross_link_restraint.seq_id_1 _item_description.description ; The sequence index for the first monomer partner in the cross link. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category and the _ihm_cross_link_restraint.seq_id_1 in the IHM_CROSS_LINK_RESTRAINT category. ; # _item.name "_ihm_cross_link_restraint.seq_id_1" _item.category_id ihm_cross_link_restraint _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_1 # _item_linked.child_name "_ihm_cross_link_restraint.seq_id_1" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_cross_link_restraint.seq_id_2 _item_description.description ; The sequence index for the second monomer partner in the cross link. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category and the _ihm_cross_link_restraint.seq_id_2 in the IHM_CROSS_LINK_RESTRAINT category. ; # _item.name "_ihm_cross_link_restraint.seq_id_2" _item.category_id ihm_cross_link_restraint _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_2 # _item_linked.child_name "_ihm_cross_link_restraint.seq_id_2" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_cross_link_restraint.atom_id_1 _item_description.description ; The atom identifier for the first monomer partner in the cross link. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; # _item.name "_ihm_cross_link_restraint.atom_id_1" _item.category_id ihm_cross_link_restraint _item.mandatory_code no # _item_type.code atcode # _item_linked.child_name "_ihm_cross_link_restraint.atom_id_1" _item_linked.parent_name "_chem_comp_atom.atom_id" # save_ # save__ihm_cross_link_restraint.atom_id_2 _item_description.description ; The atom identifier for the second monomer partner in the cross link. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; # _item.name "_ihm_cross_link_restraint.atom_id_2" _item.category_id ihm_cross_link_restraint _item.mandatory_code no # _item_type.code atcode # _item_linked.child_name "_ihm_cross_link_restraint.atom_id_2" _item_linked.parent_name "_chem_comp_atom.atom_id" # save_ # save__ihm_cross_link_restraint.restraint_type _item_description.description " The type of the cross link restraint applied." # _item.name "_ihm_cross_link_restraint.restraint_type" _item.category_id ihm_cross_link_restraint _item.mandatory_code no # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail harmonic "The restraint is satisfied if the distance between the particles is equal to the equilibrium distance" "upper bound" "The restraint is satisfied if the distance between the particles is below the distance threshold" "lower bound" "The restraint is satisfied if the distance between the particles is above the distance threshold" # save_ # save__ihm_cross_link_restraint.conditional_crosslink_flag _item_description.description " The cross link conditionality." # _item.name "_ihm_cross_link_restraint.conditional_crosslink_flag" _item.category_id ihm_cross_link_restraint _item.mandatory_code no # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail ALL "All crosslinks in the group are restrained" ANY "Any one of the crosslinks among the multiple instances in the group could be satisfied" # save_ # save__ihm_cross_link_restraint.model_granularity _item_description.description " The coarse-graining information for the crosslink implementation." # _item.name "_ihm_cross_link_restraint.model_granularity" _item.category_id ihm_cross_link_restraint _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail by-residue "Crosslink applied to the specific residue represented by the alpha carbon atom" by-feature "Crosslink applied to the closest primitive object with the highest resolution" by-atom "Crosslink applied to the specified atoms" # save_ # save__ihm_cross_link_restraint.distance_threshold _item_description.description " The distance threshold applied to this crosslink in the integrative modeling task." # _item.name "_ihm_cross_link_restraint.distance_threshold" _item.category_id ihm_cross_link_restraint _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_cross_link_restraint.psi _item_description.description ; The uncertainty in the crosslinking experimental data; may be approximated to the false positive rate. ; # _item.name "_ihm_cross_link_restraint.psi" _item.category_id ihm_cross_link_restraint _item.mandatory_code no # _item_type.code float # loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 1.0 1.0 1.0 # save_ # save__ihm_cross_link_restraint.sigma_1 _item_description.description ; The uncertainty in the position of residue 1 in the crosslink arising due to the multi-scale nature of the model represention. ; # _item.name "_ihm_cross_link_restraint.sigma_1" _item.category_id ihm_cross_link_restraint _item.mandatory_code no # _item_type.code float # save_ # save__ihm_cross_link_restraint.sigma_2 _item_description.description ; The uncertainty in the position of residue 2 in the crosslink arising due to the multi-scale nature of the model represention. ; # _item.name "_ihm_cross_link_restraint.sigma_2" _item.category_id ihm_cross_link_restraint _item.mandatory_code no # _item_type.code float # save_ # save__ihm_cross_link_restraint.pseudo_site_flag _item_description.description ; A flag indicating if the cross link involves a pseudo site that is not part of the model representation and hence will not be part of the model. However, it can be part of the input restraints. ; # _item.name "_ihm_cross_link_restraint.pseudo_site_flag" _item.category_id ihm_cross_link_restraint _item.mandatory_code no # _item_type.code ucode # loop_ _item_enumeration.value _item_enumeration.detail YES "Cross link involves a pseudo site" NO "Cross link does not involve a pseudo site" # save_ # save_ihm_cross_link_pseudo_site _category.description ; Data items in the IHM_CROSS_LINK_PSEUDO_SITE category records the details of the pseudo sites involved in the cross links. ; _category.id ihm_cross_link_pseudo_site _category.mandatory_code no # _category_key.name "_ihm_cross_link_pseudo_site.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_cross_link_pseudo_site.id _ihm_cross_link_pseudo_site.restraint_id _ihm_cross_link_pseudo_site.cross_link_partner _ihm_cross_link_pseudo_site.pseudo_site_id 1 1 1 1 2 2 1 2 3 2 2 3 4 3 2 4 5 4 1 5 6 4 2 6 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_cross_link_pseudo_site # save_ # save__ihm_cross_link_pseudo_site.id _item_description.description " A unique identifier for this category." # _item.name "_ihm_cross_link_pseudo_site.id" _item.category_id ihm_cross_link_pseudo_site _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_cross_link_pseudo_site.restraint_id _item_description.description ; An identifier for the crosslink restraint between a pair of residues. This data item is a pointer to _ihm_cross_link_restraint.id in the IHM_CROSS_LINK_RESTRAINT category. ; # _item.name "_ihm_cross_link_pseudo_site.restraint_id" _item.category_id ihm_cross_link_pseudo_site _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_cross_link_pseudo_site.restraint_id" _item_linked.parent_name "_ihm_cross_link_restraint.id" # save_ # save__ihm_cross_link_pseudo_site.cross_link_partner _item_description.description " The identity of the cross link partner corresponding to the pseudo site." # _item.name "_ihm_cross_link_pseudo_site.cross_link_partner" _item.category_id ihm_cross_link_pseudo_site _item.mandatory_code yes # _item_type.code int # loop_ _item_enumeration.value _item_enumeration.detail 1 "The first partner in the cross link as identified in the ihm_cross_link_restraint table" 2 "The second partner in the cross link as identified in the ihm_cross_link_restraint table" # save_ # save__ihm_cross_link_pseudo_site.pseudo_site_id _item_description.description ; The pseudo site identifier corresponding to the cross link partner. This data item is a pointer to _ihm_pseudo_site.id in the IHM_PSEUDO_SITE category. ; # _item.name "_ihm_cross_link_pseudo_site.pseudo_site_id" _item.category_id ihm_cross_link_pseudo_site _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_cross_link_pseudo_site.pseudo_site_id" _item_linked.parent_name "_ihm_pseudo_site.id" # save_ # save__ihm_cross_link_pseudo_site.model_id _item_description.description ; The identifier to the model that the pseudo site corresponds to. This data item is a pointer to _ihm_model_list.model_id in the IHM_MODEL_LIST category. ; # _item.name "_ihm_cross_link_pseudo_site.model_id" _item.category_id ihm_cross_link_pseudo_site _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_cross_link_pseudo_site.model_id" _item_linked.parent_name "_ihm_model_list.model_id" # save_ # save_ihm_cross_link_result _category.description ; Data items in the IHM_CROSS_LINK_RESULT category records the results of the crosslinking restraints in the IHM modeling. ; _category.id ihm_cross_link_result _category.mandatory_code no # _category_key.name "_ihm_cross_link_result.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_cross_link_result.id _ihm_cross_link_result.restraint_id _ihm_cross_link_result.ensemble_id _ihm_cross_link_result.num_models _ihm_cross_link_result.distance_threshold _ihm_cross_link_result.median_distance _ihm_cross_link_result.details 1 1 1 2885 25.0 9.6 . 2 2 1 2885 25.0 14.7 . 3 3 1 2885 25.0 16.4 . 4 4 1 2885 25.0 15.8 . 5 5 1 2885 25.0 18.9 . 6 6 1 2885 25.0 11.6 . # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_cross_link_result # save_ # save__ihm_cross_link_result.id _item_description.description " A unique identifier for the restraint/ensemble combination." # _item.name "_ihm_cross_link_result.id" _item.category_id ihm_cross_link_result _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_cross_link_result.restraint_id _item_description.description ; An identifier for the crosslink restraint between a pair of residues. This data item is a pointer to _ihm_cross_link_restraint.id in the IHM_CROSS_LINK_RESTRAINT category. ; # _item.name "_ihm_cross_link_result.restraint_id" _item.category_id ihm_cross_link_result _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_cross_link_result.restraint_id" _item_linked.parent_name "_ihm_cross_link_restraint.id" # save_ # save__ihm_cross_link_result.ensemble_id _item_description.description ; An identifier for the ensemble whose results are described. This data item is a pointer to _ihm_ensemble_info.ensemble_id in the IHM_ENSEMBLE_INFO category. ; # _item.name "_ihm_cross_link_result.ensemble_id" _item.category_id ihm_cross_link_result _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_cross_link_result.ensemble_id" _item_linked.parent_name "_ihm_ensemble_info.ensemble_id" # save_ # save__ihm_cross_link_result.num_models _item_description.description ; Number of models sampled in the integrative modeling task, for which the crosslinking distance is provided. ; # _item.name "_ihm_cross_link_result.num_models" _item.category_id ihm_cross_link_result _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_cross_link_result.distance_threshold _item_description.description " The distance threshold applied to this crosslink in the integrative modeling task." # _item.name "_ihm_cross_link_result.distance_threshold" _item.category_id ihm_cross_link_result _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_cross_link_result.median_distance _item_description.description " The median distance between the crosslinked residues in the sampled models." # _item.name "_ihm_cross_link_result.median_distance" _item.category_id ihm_cross_link_result _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_cross_link_result.details _item_description.description ; This records holds any associated details of the results of the particular crosslink restraint in the integrative modeling task. ; # _item.name "_ihm_cross_link_result.details" _item.category_id ihm_cross_link_result _item.mandatory_code no # _item_type.code text # save_ # save_ihm_cross_link_result_parameters _category.description ; Data items in the IHM_CROSS_LINK_RESULT_PARAMETERS category records the results of the crosslinking restraint parameters in the IHM modeling. ; _category.id ihm_cross_link_result_parameters _category.mandatory_code no # _category_key.name "_ihm_cross_link_result_parameters.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_cross_link_result_parameters.id _ihm_cross_link_result_parameters.restraint_id _ihm_cross_link_result_parameters.model_id _ihm_cross_link_result_parameters.psi _ihm_cross_link_result_parameters.sigma_1 _ihm_cross_link_result_parameters.sigma_2 1 1 1 0.05 0.01 0.01 2 2 1 0.05 0.01 0.01 3 3 1 0.05 0.01 0.01 4 4 2 0.05 0.01 0.01 5 5 3 0.05 0.01 0.01 6 6 4 0.05 0.01 0.01 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_cross_link_result_parameters # save_ # save__ihm_cross_link_result_parameters.id _item_description.description " A unique identifier for the restraint/model combination." # _item.name "_ihm_cross_link_result_parameters.id" _item.category_id ihm_cross_link_result_parameters _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_cross_link_result_parameters.restraint_id _item_description.description ; An identifier for the crosslink restraint between a pair of residues. This data item is a pointer to _ihm_cross_link_restraint.id in the IHM_CROSS_LINK_RESTRAINT category. ; # _item.name "_ihm_cross_link_result_parameters.restraint_id" _item.category_id ihm_cross_link_result_parameters _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_cross_link_result_parameters.restraint_id" _item_linked.parent_name "_ihm_cross_link_restraint.id" # save_ # save__ihm_cross_link_result_parameters.model_id _item_description.description ; The model number corresponding to the cross link result presented. This data item is a pointer to _ihm_model_list.model_id in the IHM_MODEL_LIST category. ; # _item.name "_ihm_cross_link_result_parameters.model_id" _item.category_id ihm_cross_link_result_parameters _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_cross_link_result_parameters.model_id" _item_linked.parent_name "_ihm_model_list.model_id" # save_ # save__ihm_cross_link_result_parameters.psi _item_description.description ; The uncertainty in the crosslinking experimental data; May be approximated to the false positive rate. ; # _item.name "_ihm_cross_link_result_parameters.psi" _item.category_id ihm_cross_link_result_parameters _item.mandatory_code no # _item_type.code float # loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 1.0 1.0 1.0 # save_ # save__ihm_cross_link_result_parameters.sigma_1 _item_description.description ; The uncertainty in the position of residue 1 in the crosslink arising due to the multi-scale nature of the model represention. ; # _item.name "_ihm_cross_link_result_parameters.sigma_1" _item.category_id ihm_cross_link_result_parameters _item.mandatory_code no # _item_type.code float # save_ # save__ihm_cross_link_result_parameters.sigma_2 _item_description.description ; The uncertainty in the position of residue 2 in the crosslink arising due to the multi-scale nature of the model represention. ; # _item.name "_ihm_cross_link_result_parameters.sigma_2" _item.category_id ihm_cross_link_result_parameters _item.mandatory_code no # _item_type.code float # save_ # save_ihm_2dem_class_average_restraint _category.description ; Data items in the IHM_2DEM_CLASS_AVERAGE_RESTRAINT category records the details of the 2DEM class averages used in the IHM modeling. ; _category.id ihm_2dem_class_average_restraint _category.mandatory_code no # _category_key.name "_ihm_2dem_class_average_restraint.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; _ihm_2dem_class_average_restraint.id 1 _ihm_2dem_class_average_restraint.dataset_list_id 4 _ihm_2dem_class_average_restraint.number_raw_micrographs 200 _ihm_2dem_class_average_restraint.pixel_size_width 5.91 _ihm_2dem_class_average_restraint.pixel_size_height 5.91 _ihm_2dem_class_average_restraint.image_resolution 30.0 _ihm_2dem_class_average_restraint.image_segment_flag No _ihm_2dem_class_average_restraint.number_of_projections 400 _ihm_2dem_class_average_restraint.struct_assembly_id 1 _ihm_2dem_class_average_restraint.details . ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_2dem_class_average_restraint # save_ # save__ihm_2dem_class_average_restraint.id _item_description.description " A unique identifier for the 2dem class average." # _item.name "_ihm_2dem_class_average_restraint.id" _item.category_id ihm_2dem_class_average_restraint _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_2dem_class_average_restraint.dataset_list_id _item_description.description ; Identifier to the 2dem class average dataset. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_2dem_class_average_restraint.dataset_list_id" _item.category_id ihm_2dem_class_average_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_2dem_class_average_restraint.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save__ihm_2dem_class_average_restraint.number_raw_micrographs _item_description.description " The number of raw micrographs used to obtain the class average." # _item.name "_ihm_2dem_class_average_restraint.number_raw_micrographs" _item.category_id ihm_2dem_class_average_restraint _item.mandatory_code no # _item_type.code int # save_ # save__ihm_2dem_class_average_restraint.pixel_size_width _item_description.description ; Pixel size width of the 2dem class average image. While fitting the model to the image, _ihm_2dem_class_average_restraint.pixel_size_width is used along with _ihm_2dem_class_average_restraint.pixel_size_height to scale the image. ; # _item.name "_ihm_2dem_class_average_restraint.pixel_size_width" _item.category_id ihm_2dem_class_average_restraint _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_2dem_class_average_restraint.pixel_size_height _item_description.description ; Pixel size height of the 2dem class average image. While fitting the model to the image, _ihm_2dem_class_average_restraint.pixel_size_height is used along with _ihm_2dem_class_average_restraint.pixel_size_width to scale the image. ; # _item.name "_ihm_2dem_class_average_restraint.pixel_size_height" _item.category_id ihm_2dem_class_average_restraint _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_2dem_class_average_restraint.image_resolution _item_description.description " Resolution of the 2dem class average." # _item.name "_ihm_2dem_class_average_restraint.image_resolution" _item.category_id ihm_2dem_class_average_restraint _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_2dem_class_average_restraint.image_segment_flag _item_description.description ; A flag that indicates whether or not the 2DEM class average image is segmented i.e., whether the whole image is used or only a portion of it is used (by masking or by other means) as restraint in the modeling. ; # _item.name "_ihm_2dem_class_average_restraint.image_segment_flag" _item.category_id ihm_2dem_class_average_restraint _item.mandatory_code no # _item_type.code ucode # loop_ _item_enumeration.value _item_enumeration.detail YES "Image is masked; only a portion of the image is used" NO "Image is not masked; the entire image is used" # save_ # save__ihm_2dem_class_average_restraint.number_of_projections _item_description.description " Number of 2D projections of the model used in the fitting." # _item.name "_ihm_2dem_class_average_restraint.number_of_projections" _item.category_id ihm_2dem_class_average_restraint _item.mandatory_code no # _item_type.code int # save_ # save__ihm_2dem_class_average_restraint.struct_assembly_id _item_description.description ; An indicator to whether the whole assembly that is modeled is fit into the image or if only a subset of the structural assembly is fit into the image. This data item is a pointer to _ihm_struct_assembly.id in the IHM_STRUCT_ASSEMBLY category. The IHM_STRUCT_ASSEMBLY category provides the details regarding the different structural assemblies used in the modeling. The default value for this data item is "1" indicating that the entire assembly being modeled is fit into the EM data. ; # _item.name "_ihm_2dem_class_average_restraint.struct_assembly_id" _item.category_id ihm_2dem_class_average_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_2dem_class_average_restraint.struct_assembly_id" _item_linked.parent_name "_ihm_struct_assembly.id" # _item_default.value 1 # save_ # save__ihm_2dem_class_average_restraint.details _item_description.description " Details of how the 2DEM restraint is applied in the modeling algorithm." # _item.name "_ihm_2dem_class_average_restraint.details" _item.category_id ihm_2dem_class_average_restraint _item.mandatory_code no # _item_type.code text # _item_examples.case ; The 2DEM restraint fits a given model to an 2DEM class average and computes a score that quantifies the match. The computation proceeds in three stages: generation of 3D model projections on a 2D grid, alignment of the model projections and the 2DEM class average image, and calculation of the best fitting score. ; # save_ # save_ihm_2dem_class_average_fitting _category.description ; Data items in the IHM_2DEM_CLASS_AVERAGE_FITTING category records the details of the fitting of the model to the 2DEM class averages used in the IHM modeling. The following conventions are recommended while generating the rotation matrix and translation vector for transformation. - The model is rotated and translated to fit to the 2DEM image. - The 2DEM image should be in the XY plane. - The lower left image corner (image pixel index 0,0) should be at x,y,z = (0,0,0). - The 2D image is scaled by the _ihm_2dem_class_average_restraint.pixel_size_width and _ihm_2dem_class_average_restraint.pixel_size_height from the IHM_2DEM_CLASS_AVERAGE_RESTRAINT table. - The transformation is applied after the scaling and hence the translation vector should account for the scaling. - There are no specifications for Z translations i.e., how far the image should be from the model while projecting. It may be set to zero. ; _category.id ihm_2dem_class_average_fitting _category.mandatory_code no # _category_key.name "_ihm_2dem_class_average_fitting.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; _ihm_2dem_class_average_fitting.id 1 _ihm_2dem_class_average_fitting.restraint_id 1 _ihm_2dem_class_average_fitting.model_id 1 _ihm_2dem_class_average_fitting.cross_correlation_coefficient 0.9 _ihm_2dem_class_average_fitting.rot_matrix[1][1] 1.0 _ihm_2dem_class_average_fitting.rot_matrix[2][1] 0.0 _ihm_2dem_class_average_fitting.rot_matrix[3][1] 0.0 _ihm_2dem_class_average_fitting.rot_matrix[1][2] 0.0 _ihm_2dem_class_average_fitting.rot_matrix[2][2] 1.0 _ihm_2dem_class_average_fitting.rot_matrix[3][2] 0.0 _ihm_2dem_class_average_fitting.rot_matrix[1][3] 0.0 _ihm_2dem_class_average_fitting.rot_matrix[2][3] 0.0 _ihm_2dem_class_average_fitting.rot_matrix[3][3] 1.0 _ihm_2dem_class_average_fitting.tr_vector[1] 0.0 _ihm_2dem_class_average_fitting.tr_vector[2] 0.0 _ihm_2dem_class_average_fitting.tr_vector[3] 0.0 ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_2dem_class_average_fitting # save_ # save__ihm_2dem_class_average_fitting.id _item_description.description " A unique identifier for the 2dem class average fitting data." # _item.name "_ihm_2dem_class_average_fitting.id" _item.category_id ihm_2dem_class_average_fitting _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_2dem_class_average_fitting.restraint_id _item_description.description ; Identifier to the 2dem class average restraint. This data item is a pointer to the _ihm_2dem_class_average_restraint.id in the IHM_2DEM_CLASS_AVERAGE_RESTRAINT category. ; # _item.name "_ihm_2dem_class_average_fitting.restraint_id" _item.category_id ihm_2dem_class_average_fitting _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_2dem_class_average_fitting.restraint_id" _item_linked.parent_name "_ihm_2dem_class_average_restraint.id" # save_ # save__ihm_2dem_class_average_fitting.model_id _item_description.description ; The model number corresponding to the 2DEM fitting result presented. This data item is a pointer to _ihm_model_list.model_id in the IHM_MODEL_LIST category. ; # _item.name "_ihm_2dem_class_average_fitting.model_id" _item.category_id ihm_2dem_class_average_fitting _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_2dem_class_average_fitting.model_id" _item_linked.parent_name "_ihm_model_list.model_id" # save_ # save__ihm_2dem_class_average_fitting.cross_correlation_coefficient _item_description.description " The cross correlation coefficient corresponding to the model to image fitting." # _item.name "_ihm_2dem_class_average_fitting.cross_correlation_coefficient" _item.category_id ihm_2dem_class_average_fitting _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code float # save_ # save__ihm_2dem_class_average_fitting.rot_matrix[1][1] _item_description.description " Data item [1][1] of the rotation matrix used in the fitting of the model to the image." # _item.name "_ihm_2dem_class_average_fitting.rot_matrix[1][1]" _item.category_id ihm_2dem_class_average_fitting _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_2dem_class_average_fitting.rot_matrix[2][1] _item_description.description " Data item [2][1] of the rotation matrix used in the fitting of the model to the image." # _item.name "_ihm_2dem_class_average_fitting.rot_matrix[2][1]" _item.category_id ihm_2dem_class_average_fitting _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_2dem_class_average_fitting.rot_matrix[3][1] _item_description.description " Data item [3][1] of the rotation matrix used in the fitting of the model to the image." # _item.name "_ihm_2dem_class_average_fitting.rot_matrix[3][1]" _item.category_id ihm_2dem_class_average_fitting _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_2dem_class_average_fitting.rot_matrix[1][2] _item_description.description " Data item [1][2] of the rotation matrix used in the fitting of the model to the image." # _item.name "_ihm_2dem_class_average_fitting.rot_matrix[1][2]" _item.category_id ihm_2dem_class_average_fitting _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_2dem_class_average_fitting.rot_matrix[2][2] _item_description.description " Data item [2][2] of the rotation matrix used in the fitting of the model to the image." # _item.name "_ihm_2dem_class_average_fitting.rot_matrix[2][2]" _item.category_id ihm_2dem_class_average_fitting _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_2dem_class_average_fitting.rot_matrix[3][2] _item_description.description " Data item [3][2] of the rotation matrix used in the fitting of the model to the image." # _item.name "_ihm_2dem_class_average_fitting.rot_matrix[3][2]" _item.category_id ihm_2dem_class_average_fitting _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_2dem_class_average_fitting.rot_matrix[1][3] _item_description.description " Data item [1][3] of the rotation matrix used in the fitting of the model to the image." # _item.name "_ihm_2dem_class_average_fitting.rot_matrix[1][3]" _item.category_id ihm_2dem_class_average_fitting _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_2dem_class_average_fitting.rot_matrix[2][3] _item_description.description " Data item [2][3] of the rotation matrix used in the fitting of the model to the image." # _item.name "_ihm_2dem_class_average_fitting.rot_matrix[2][3]" _item.category_id ihm_2dem_class_average_fitting _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_2dem_class_average_fitting.rot_matrix[3][3] _item_description.description " Data item [3][3] of the rotation matrix used in the fitting of the model to the image." # _item.name "_ihm_2dem_class_average_fitting.rot_matrix[3][3]" _item.category_id ihm_2dem_class_average_fitting _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_2dem_class_average_fitting.tr_vector[1] _item_description.description " Data item [1] of the tranlation vector used in the fitting of the model to the image." # _item.name "_ihm_2dem_class_average_fitting.tr_vector[1]" _item.category_id ihm_2dem_class_average_fitting _item.mandatory_code no # _item_sub_category.id vector # _item_type.code float # save_ # save__ihm_2dem_class_average_fitting.tr_vector[2] _item_description.description " Data item [2] of the tranlation vector used in the fitting of the model to the image." # _item.name "_ihm_2dem_class_average_fitting.tr_vector[2]" _item.category_id ihm_2dem_class_average_fitting _item.mandatory_code no # _item_sub_category.id vector # _item_type.code float # save_ # save__ihm_2dem_class_average_fitting.tr_vector[3] _item_description.description " Data item [3] of the tranlation vector used in the fitting of the model to the image." # _item.name "_ihm_2dem_class_average_fitting.tr_vector[3]" _item.category_id ihm_2dem_class_average_fitting _item.mandatory_code no # _item_sub_category.id vector # _item_type.code float # save_ # save_ihm_3dem_restraint _category.description ; Data items in the IHM_3DEM_RESTRAINT category records the details of the 3DEM maps used as restraints in the IHM modeling. ; _category.id ihm_3dem_restraint _category.mandatory_code no # _category_key.name "_ihm_3dem_restraint.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; _ihm_3dem_restraint.id 1 _ihm_3dem_restraint.dataset_list_id 3 _ihm_3dem_restraint.model_id 1 _ihm_3dem_restraint.struct_assembly_id 1 _ihm_3dem_restraint.fitting_method 'Gaussian mixture models' _ihm_3dem_restraint.number_of_gaussians 10 _ihm_3dem_restraint.map_segment_flag No _ihm_3dem_restraint.cross_correlation_coefficient 0.8 _ihm_3dem_restraint.fitting_method_citation_id 5 _ihm_3dem_restraint.details . ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_3dem_restraint # save_ # save__ihm_3dem_restraint.id _item_description.description " A unique identifier for the 3DEM restraint description." # _item.name "_ihm_3dem_restraint.id" _item.category_id ihm_3dem_restraint _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_3dem_restraint.dataset_list_id _item_description.description ; Identifier to the 3DEM map used. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_3dem_restraint.dataset_list_id" _item.category_id ihm_3dem_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_3dem_restraint.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save__ihm_3dem_restraint.model_id _item_description.description ; The model number corresponding to the 3DEM fitting result presented. This data item is a pointer to _ihm_model_list.model_id in the IHM_MODEL_LIST category. ; # _item.name "_ihm_3dem_restraint.model_id" _item.category_id ihm_3dem_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_3dem_restraint.model_id" _item_linked.parent_name "_ihm_model_list.model_id" # save_ # save__ihm_3dem_restraint.struct_assembly_id _item_description.description ; An indicator to whether the whole assembly that is modeled is fit into the 3DEM map or if only a subset of the structural assembly is fit into the map. This data item is a pointer to _ihm_struct_assembly.id in the IHM_STRUCT_ASSEMBLY category. The IHM_STRUCT_ASSEMBLY category provides the details regarding the different structural assemblies used in the modeling. The default value for this data item is "1" indicating that the entire assembly being modeled is fit into the EM map. ; # _item.name "_ihm_3dem_restraint.struct_assembly_id" _item.category_id ihm_3dem_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_3dem_restraint.struct_assembly_id" _item_linked.parent_name "_ihm_struct_assembly.id" # _item_default.value 1 # save_ # save__ihm_3dem_restraint.fitting_method _item_description.description " Method used to fit the model to the 3DEM map." # _item.name "_ihm_3dem_restraint.fitting_method" _item.category_id ihm_3dem_restraint _item.mandatory_code no # _item_type.code line # loop_ _item_examples.case "Gaussian mixture model" "Local refinement" "Flexible fitting" Other # save_ # save__ihm_3dem_restraint.number_of_gaussians _item_description.description ; In case of Gaussian mixture models, the number of gaussians is a parameter used to covert the 3DEM maps and models into GMMs. This captures the level of granularity used in representing the maps and/or models as 3D Gaussians. ; # _item.name "_ihm_3dem_restraint.number_of_gaussians" _item.category_id ihm_3dem_restraint _item.mandatory_code no # _item_type.code int # save_ # save__ihm_3dem_restraint.map_segment_flag _item_description.description ; A flag that indicates whether or not the 3DEM map is segmented i.e., whether the whole map is used or only a portion of it is used (by masking or by other means) as restraint in the modeling. ; # _item.name "_ihm_3dem_restraint.map_segment_flag" _item.category_id ihm_3dem_restraint _item.mandatory_code no # _item_type.code ucode # loop_ _item_enumeration.value _item_enumeration.detail YES "Map is masked; only a portion of the map is used" NO "Map is not masked; the entire map is used" # save_ # save__ihm_3dem_restraint.cross_correlation_coefficient _item_description.description " The cross correlation coefficient corresponding to the model to map fitting." # _item.name "_ihm_3dem_restraint.cross_correlation_coefficient" _item.category_id ihm_3dem_restraint _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code float # save_ # save__ihm_3dem_restraint.fitting_method_citation_id _item_description.description ; The citation id of the citation for the fitting method used. This data item is a pointer to _citation.id in the CITATION category. ; # _item.name "_ihm_3dem_restraint.fitting_method_citation_id" _item.category_id ihm_3dem_restraint _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_ihm_3dem_restraint.fitting_method_citation_id" _item_linked.parent_name "_citation.id" # save_ # save__ihm_3dem_restraint.details _item_description.description " Additional details regarding the model to map fitting." # _item.name "_ihm_3dem_restraint.details" _item.category_id ihm_3dem_restraint _item.mandatory_code no # _item_type.code text # _item_examples.case ; The Nup-84 models generated and the 3DEM maps are converted to 3D Gaussians using Gaussian mixture models (GMMs). The GMMs are then compared to obtain a 3D fit of the map and the model. ; # save_ # save_ihm_sas_restraint _category.description ; Data items in the IHM_SAS_RESTRAINT category records the details of the SAS data used as restraints in the IHM modeling. ; _category.id ihm_sas_restraint _category.mandatory_code no # _category_key.name "_ihm_sas_restraint.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; _ihm_sas_restraint.id 1 _ihm_sas_restraint.dataset_list_id 6 _ihm_sas_restraint.model_id 1 _ihm_sas_restraint.struct_assembly_id 1 _ihm_sas_restraint.profile_segment_flag NO _ihm_sas_restraint.fitting_atom_type 'Heavy atoms' _ihm_sas_restraint.fitting_method 'FoXS' _ihm_sas_restraint.fitting_state 'Single' _ihm_sas_restraint.radius_of_gyration 21.07 _ihm_sas_restraint.chi_value 4.69 _ihm_sas_restraint.details . ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_sas_restraint # save_ # save__ihm_sas_restraint.id _item_description.description " A unique identifier for the SAS restraint description." # _item.name "_ihm_sas_restraint.id" _item.category_id ihm_sas_restraint _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_sas_restraint.dataset_list_id _item_description.description ; Identifier to the SAS data used. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_sas_restraint.dataset_list_id" _item.category_id ihm_sas_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_sas_restraint.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save__ihm_sas_restraint.model_id _item_description.description ; The model number corresponding to the SAS fitting result presented. This data item is a pointer to _ihm_model_list.model_id in the IHM_MODEL_LIST category. ; # _item.name "_ihm_sas_restraint.model_id" _item.category_id ihm_sas_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_sas_restraint.model_id" _item_linked.parent_name "_ihm_model_list.model_id" # save_ # save__ihm_sas_restraint.struct_assembly_id _item_description.description ; An indicator to whether the whole assembly that is modeled is fit into the SAS data or if only a subset of the structural assembly is fit into the data. This data item is a pointer to _ihm_struct_assembly.id in the IHM_STRUCT_ASSEMBLY category. The IHM_STRUCT_ASSEMBLY category provides the details regarding the different structural assemblies used in the modeling. The default value for this data item is "1" indicating that the entire assembly being modeled is fit into the SAS data. ; # _item.name "_ihm_sas_restraint.struct_assembly_id" _item.category_id ihm_sas_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_sas_restraint.struct_assembly_id" _item_linked.parent_name "_ihm_struct_assembly.id" # _item_default.value 1 # save_ # save__ihm_sas_restraint.profile_segment_flag _item_description.description ; A flag that indicates whether or not the SAS profile is segmented i.e., whether the whole SAS profile is used or only a portion of it is used (by masking or by other means) as restraint in the modeling. ; # _item.name "_ihm_sas_restraint.profile_segment_flag" _item.category_id ihm_sas_restraint _item.mandatory_code no # _item_type.code ucode # loop_ _item_enumeration.value _item_enumeration.detail YES "SAS profile is masked; only a portion of the SAS data is used" NO "SAS profile is not masked; the entire SAS data is used" # save_ # save__ihm_sas_restraint.fitting_atom_type _item_description.description " The type of atoms in the model fit to the SAS data." # _item.name "_ihm_sas_restraint.fitting_atom_type" _item.category_id ihm_sas_restraint _item.mandatory_code no # _item_type.code line # loop_ _item_examples.case "C-alpha atoms" "Heavy atoms" "All atoms" # save_ # save__ihm_sas_restraint.fitting_method _item_description.description " The method used for fitting the model to the SAS data." # _item.name "_ihm_sas_restraint.fitting_method" _item.category_id ihm_sas_restraint _item.mandatory_code no # _item_type.code line # loop_ _item_examples.case DAMMIF FoXS MultiFoXS "Minimal Ensemble Search" Other # save_ # save__ihm_sas_restraint.fitting_state _item_description.description " An indicator to single or multiple state fitting." # _item.name "_ihm_sas_restraint.fitting_state" _item.category_id ihm_sas_restraint _item.mandatory_code no # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail Single "Single-state fitting" Multiple "Multi-state fitting" # save_ # save__ihm_sas_restraint.radius_of_gyration _item_description.description " Radius of gyration obtained from the SAS profile, if used as input restraint." # _item.name "_ihm_sas_restraint.radius_of_gyration" _item.category_id ihm_sas_restraint _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_sas_restraint.chi_value _item_description.description " The chi value resulting from fitting the model to the SAS data." # _item.name "_ihm_sas_restraint.chi_value" _item.category_id ihm_sas_restraint _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_sas_restraint.details _item_description.description " Additional details regarding the SAS restraint used." # _item.name "_ihm_sas_restraint.details" _item.category_id ihm_sas_restraint _item.mandatory_code no # _item_type.code text # save_ # save_ihm_hdx_restraint _category.description ; Data items in the IHM_HDX_RESTRAINT category captures the details of restraints derived from Hydrogen-Deuterium Exchange experiments. ; _category.id ihm_hdx_restraint _category.mandatory_code no # _category_key.name "_ihm_hdx_restraint.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_hdx_restraint.id _ihm_hdx_restraint.feature_id _ihm_hdx_restraint.protection_factor _ihm_hdx_restraint.dataset_list_id _ihm_hdx_restraint.details 1 1 1.0 6 . 2 2 1.0 6 . 3 3 1.0 6 . 4 4 1.0 6 . 5 5 1.0 6 . 6 6 1.0 6 . 7 7 1.0 6 . 8 8 1.0 6 . 9 9 1.0 6 . # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_hdx_restraint # save_ # save__ihm_hdx_restraint.id _item_description.description " A unique identifier for the category." # _item.name "_ihm_hdx_restraint.id" _item.category_id ihm_hdx_restraint _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_hdx_restraint.feature_id _item_description.description ; Identifier for the peptide / residue feature. This data item is a pointer to _ihm_feature_list.feature_id in the IHM_FEATURE_LIST category. ; # _item.name "_ihm_hdx_restraint.feature_id" _item.category_id ihm_hdx_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_hdx_restraint.feature_id" _item_linked.parent_name "_ihm_feature_list.feature_id" # save_ # save__ihm_hdx_restraint.protection_factor _item_description.description ; The value of the protection factor determined from HDX experiments. These are reported as log(protection factor). Protection factors are scaling factors and are unitless. ; # _item.name "_ihm_hdx_restraint.protection_factor" _item.category_id ihm_hdx_restraint _item.mandatory_code no # _item_type.code float # save_ # save__ihm_hdx_restraint.dataset_list_id _item_description.description ; Identifier to the HDX input data from which the restraints are derived. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_hdx_restraint.dataset_list_id" _item.category_id ihm_hdx_restraint _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_hdx_restraint.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save__ihm_hdx_restraint.details _item_description.description " Additional details regarding the HDX restraint." # _item.name "_ihm_hdx_restraint.details" _item.category_id ihm_hdx_restraint _item.mandatory_code no # _item_type.code text # save_ # save_ihm_starting_model_coord _category.description ; Data items in the IHM_STARTING_MODEL_COORD category records the coordinates for structural templates used as starting inputs in the integrative model building tasks. ; _category.id ihm_starting_model_coord _category.mandatory_code no # _category_key.name "_ihm_starting_model_coord.ordinal_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_starting_model_coord.starting_model_id _ihm_starting_model_coord.group_PDB _ihm_starting_model_coord.id _ihm_starting_model_coord.type_symbol _ihm_starting_model_coord.atom_id _ihm_starting_model_coord.comp_id _ihm_starting_model_coord.entity_id _ihm_starting_model_coord.asym_id _ihm_starting_model_coord.seq_id _ihm_starting_model_coord.Cartn_x _ihm_starting_model_coord.Cartn_y _ihm_starting_model_coord.Cartn_z _ihm_starting_model_coord.B_iso_or_equiv _ihm_starting_model_coord.formal_charge _ihm_starting_model_coord.ordinal_id Nup84-m1 ATOM 1 N N TYR 1 A 7 -9.852 10.605 -6.336 91.82 . 1 Nup84-m1 ATOM 2 C CA TYR 1 A 7 -8.986 11.688 -5.817 91.82 . 2 Nup84-m1 ATOM 3 C CB TYR 1 A 7 -7.787 11.073 -5.072 91.82 . 3 Nup84-m1 ATOM 4 C CG TYR 1 A 7 -6.741 12.117 -4.873 91.82 . 4 Nup84-m1 ATOM 5 C CD1 TYR 1 A 7 -6.906 13.168 -3.998 91.82 . 5 Nup84-m1 ATOM 6 C CD2 TYR 1 A 7 -5.561 12.013 -5.571 91.82 . 6 Nup84-m1 ATOM 7 C CE1 TYR 1 A 7 -5.91 14.108 -3.843 91.82 . 7 Nup84-m1 ATOM 8 C CE2 TYR 1 A 7 -4.566 12.945 -5.421 91.82 . 8 Nup84-m1 ATOM 9 C CZ TYR 1 A 7 -4.738 13.997 -4.558 91.82 . 9 Nup84-m1 ATOM 10 O OH TYR 1 A 7 -3.708 14.949 -4.411 91.82 . 10 Nup84-m1 ATOM 11 C C TYR 1 A 7 -8.513 12.596 -6.909 91.82 . 11 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_starting_model_coord # save_ # save__ihm_starting_model_coord.ordinal_id _item_description.description " A unique identifier for this coordinate position." # _item.name "_ihm_starting_model_coord.ordinal_id" _item.category_id ihm_starting_model_coord _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_starting_model_coord.starting_model_id _item_description.description ; The identifier for the starting structural model. This data item is a pointer to _ihm_starting_model_details.starting_model_id in the IHM_STARTING_MODEL_DETAILS category. ; # _item.name "_ihm_starting_model_coord.starting_model_id" _item.category_id ihm_starting_model_coord _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_starting_model_coord.starting_model_id" _item_linked.parent_name "_ihm_starting_model_details.starting_model_id" # save_ # save__ihm_starting_model_coord.group_PDB _item_description.description ; The group of atoms to which the atom site in the starting model belongs. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. ; # _item.name "_ihm_starting_model_coord.group_PDB" _item.category_id ihm_starting_model_coord _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value ATOM HETATM # save_ # save__ihm_starting_model_coord.id _item_description.description " The serial number for this coordinate position." # _item.name "_ihm_starting_model_coord.id" _item.category_id ihm_starting_model_coord _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_starting_model_coord.type_symbol _item_description.description " The atom type symbol(element symbol) corresponding to this coordinate position." # _item.name "_ihm_starting_model_coord.type_symbol" _item.category_id ihm_starting_model_coord _item.mandatory_code yes # _item_type.code code # save_ # save__ihm_starting_model_coord.entity_id _item_description.description ; The entity identifier corresponding to this coordinate position. This data item is a pointer to _entity.id in the ENTITY category. ; # _item.name "_ihm_starting_model_coord.entity_id" _item.category_id ihm_starting_model_coord _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_starting_model_coord.entity_id" _item_linked.parent_name "_entity.id" # save_ # save__ihm_starting_model_coord.atom_id _item_description.description ; The atom identifier/name corresponding to this coordinate position. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; # _item.name "_ihm_starting_model_coord.atom_id" _item.category_id ihm_starting_model_coord _item.mandatory_code yes # _item_type.code atcode # _item_linked.child_name "_ihm_starting_model_coord.atom_id" _item_linked.parent_name "_chem_comp_atom.atom_id" # save_ # save__ihm_starting_model_coord.comp_id _item_description.description ; The component identifier corresponding to this coordinate position. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; # _item.name "_ihm_starting_model_coord.comp_id" _item.category_id ihm_starting_model_coord _item.mandatory_code yes # _item_type.code ucode # _item_linked.child_name "_ihm_starting_model_coord.comp_id" _item_linked.parent_name "_chem_comp.id" # save_ # save__ihm_starting_model_coord.seq_id _item_description.description ; The sequence index corresponding this to coordinate position. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_starting_model_coord.seq_id" _item.category_id ihm_starting_model_coord _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label # _item_linked.child_name "_ihm_starting_model_coord.seq_id" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_starting_model_coord.asym_id _item_description.description ; The asym/strand id corresponding to this coordinate position. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_starting_model_coord.asym_id" _item.category_id ihm_starting_model_coord _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_starting_model_coord.asym_id" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_starting_model_coord.Cartn_x _item_description.description " The Cartesian X component corresponding to this coordinate position." # _item.name "_ihm_starting_model_coord.Cartn_x" _item.category_id ihm_starting_model_coord _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_starting_model_coord.Cartn_y _item_description.description " The Cartesian Y component corresponding to this coordinate position." # _item.name "_ihm_starting_model_coord.Cartn_y" _item.category_id ihm_starting_model_coord _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_starting_model_coord.Cartn_z _item_description.description " The Cartesian Z component corresponding to this coordinate position." # _item.name "_ihm_starting_model_coord.Cartn_z" _item.category_id ihm_starting_model_coord _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_starting_model_coord.B_iso_or_equiv _item_description.description " The isotropic temperature factor corresponding to this coordinate position." # _item.name "_ihm_starting_model_coord.B_iso_or_equiv" _item.category_id ihm_starting_model_coord _item.mandatory_code no # _item_type.code float # _item_units.code 8pi2_angstroms_squared # save_ # save__ihm_starting_model_coord.formal_charge _item_description.description " The formal charge corresponding to this coordinate position." # _item.name "_ihm_starting_model_coord.formal_charge" _item.category_id ihm_starting_model_coord _item.mandatory_code no # _item_type.code int # save_ # save_ihm_sphere_obj_site _category.description ; Data items in the IHM_SPHERE_OBJ_SITE category records the details of the spherical objects modeled in the integrative structural model. ; _category.id ihm_sphere_obj_site _category.mandatory_code no # _category_key.name "_ihm_sphere_obj_site.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_sphere_obj_site.id _ihm_sphere_obj_site.entity_id _ihm_sphere_obj_site.seq_id_begin _ihm_sphere_obj_site.seq_id_end _ihm_sphere_obj_site.asym_id _ihm_sphere_obj_site.Cartn_x _ihm_sphere_obj_site.Cartn_y _ihm_sphere_obj_site.Cartn_z _ihm_sphere_obj_site.object_radius _ihm_sphere_obj_site.rmsf _ihm_sphere_obj_site.model_id 1 1 1 6 A 1.0 1.0 1.0 1.0 . 1 2 1 7 7 A 1.0 1.0 1.0 1.0 . 1 3 1 8 8 A 1.0 1.0 1.0 1.0 . 1 4 1 9 9 A 1.0 1.0 1.0 1.0 . 1 5 1 10 10 A 1.0 1.0 1.0 1.0 . 1 6 1 11 11 A 1.0 1.0 1.0 1.0 . 1 7 1 12 12 A 1.0 1.0 1.0 1.0 . 1 8 1 13 13 A 1.0 1.0 1.0 1.0 . 1 9 1 14 14 A 1.0 1.0 1.0 1.0 . 1 10 1 15 15 A 1.0 1.0 1.0 1.0 . 1 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_sphere_obj_site # save_ # save__ihm_sphere_obj_site.id _item_description.description " A unique identifier for this pseudo atom / sphere object." # _item.name "_ihm_sphere_obj_site.id" _item.category_id ihm_sphere_obj_site _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_sphere_obj_site.entity_id _item_description.description ; The entity identifier corresponding to this sphere object. This data item is a pointer to _entity.id in the ENTITY category. ; # _item.name "_ihm_sphere_obj_site.entity_id" _item.category_id ihm_sphere_obj_site _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_sphere_obj_site.entity_id" _item_linked.parent_name "_entity.id" # save_ # save__ihm_sphere_obj_site.seq_id_begin _item_description.description ; The leading sequence index corresponding to this sphere object. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_sphere_obj_site.seq_id_begin" _item.category_id ihm_sphere_obj_site _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_begin # _item_linked.child_name "_ihm_sphere_obj_site.seq_id_begin" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_sphere_obj_site.seq_id_end _item_description.description ; The trailing sequence index corresponding to this sphere object. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_sphere_obj_site.seq_id_end" _item.category_id ihm_sphere_obj_site _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_end # _item_linked.child_name "_ihm_sphere_obj_site.seq_id_end" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_sphere_obj_site.asym_id _item_description.description ; An asym/strand identifier corresponding to this sphere object. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_sphere_obj_site.asym_id" _item.category_id ihm_sphere_obj_site _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_sphere_obj_site.asym_id" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_sphere_obj_site.Cartn_x _item_description.description " The Cartesian X component corresponding to this sphere object." # _item.name "_ihm_sphere_obj_site.Cartn_x" _item.category_id ihm_sphere_obj_site _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # loop_ _item_dependent.dependent_name "_ihm_sphere_obj_site.Cartn_y" "_ihm_sphere_obj_site.Cartn_z" # save_ # save__ihm_sphere_obj_site.Cartn_y _item_description.description " The Cartesian Y component corresponding to this sphere object." # _item.name "_ihm_sphere_obj_site.Cartn_y" _item.category_id ihm_sphere_obj_site _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # loop_ _item_dependent.dependent_name "_ihm_sphere_obj_site.Cartn_x" "_ihm_sphere_obj_site.Cartn_z" # save_ # save__ihm_sphere_obj_site.Cartn_z _item_description.description " The Cartesian Z component corresponding to this sphere object." # _item.name "_ihm_sphere_obj_site.Cartn_z" _item.category_id ihm_sphere_obj_site _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # loop_ _item_dependent.dependent_name "_ihm_sphere_obj_site.Cartn_x" "_ihm_sphere_obj_site.Cartn_y" # save_ # save__ihm_sphere_obj_site.object_radius _item_description.description " The radius associated with the primitive sphere object at this position." # _item.name "_ihm_sphere_obj_site.object_radius" _item.category_id ihm_sphere_obj_site _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_sphere_obj_site.rmsf _item_description.description ; The Root Mean Square Fluctuation (RMSF) observed in the primitive sphere object at this position. ; # _item.name "_ihm_sphere_obj_site.rmsf" _item.category_id ihm_sphere_obj_site _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_sphere_obj_site.model_id _item_description.description ; The model id corresponding to the sphere object. This data item is a pointer to _ihm_model_list.model_id in the IHM_MODEL_LIST category. ; # _item.name "_ihm_sphere_obj_site.model_id" _item.category_id ihm_sphere_obj_site _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_sphere_obj_site.model_id" _item_linked.parent_name "_ihm_model_list.model_id" # save_ # save_ihm_gaussian_obj_site _category.description ; Data items in the IHM_GAUSSIAN_OBJ_SITE category records the details of the gaussian objects modeled in the integrative structural model. ; _category.id ihm_gaussian_obj_site _category.mandatory_code no # _category_key.name "_ihm_gaussian_obj_site.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_gaussian_obj_site.id _ihm_gaussian_obj_site.entity_id _ihm_gaussian_obj_site.seq_id_begin _ihm_gaussian_obj_site.seq_id_end _ihm_gaussian_obj_site.asym_id _ihm_gaussian_obj_site.mean_Cartn_x _ihm_gaussian_obj_site.mean_Cartn_y _ihm_gaussian_obj_site.mean_Cartn_z _ihm_gaussian_obj_site.weight _ihm_gaussian_obj_site.covariance_matrix[1][1] _ihm_gaussian_obj_site.covariance_matrix[1][2] _ihm_gaussian_obj_site.covariance_matrix[1][3] _ihm_gaussian_obj_site.covariance_matrix[2][1] _ihm_gaussian_obj_site.covariance_matrix[2][2] _ihm_gaussian_obj_site.covariance_matrix[2][3] _ihm_gaussian_obj_site.covariance_matrix[3][1] _ihm_gaussian_obj_site.covariance_matrix[3][2] _ihm_gaussian_obj_site.covariance_matrix[3][3] _ihm_gaussian_obj_site.model_id 1 1 1 6 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 2 1 7 7 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 3 1 8 8 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 4 1 9 9 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 5 1 10 10 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 6 1 11 11 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 7 1 12 12 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 8 1 13 13 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 9 1 14 14 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 10 1 15 15 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_gaussian_obj_site # save_ # save__ihm_gaussian_obj_site.id _item_description.description " A unique identifier for this gaussian object in the model." # _item.name "_ihm_gaussian_obj_site.id" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_gaussian_obj_site.entity_id _item_description.description ; The entity identifier corresponding to this gaussian object. This data item is a pointer to _entity.id in the ENTITY category. ; # _item.name "_ihm_gaussian_obj_site.entity_id" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_gaussian_obj_site.entity_id" _item_linked.parent_name "_entity.id" # save_ # save__ihm_gaussian_obj_site.seq_id_begin _item_description.description ; The leading sequence index corresponding to this gaussian object. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_gaussian_obj_site.seq_id_begin" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_begin # _item_linked.child_name "_ihm_gaussian_obj_site.seq_id_begin" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_gaussian_obj_site.seq_id_end _item_description.description ; The trailing sequence index corresponding to this gaussian object. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_gaussian_obj_site.seq_id_end" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_end # _item_linked.child_name "_ihm_gaussian_obj_site.seq_id_end" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_gaussian_obj_site.asym_id _item_description.description ; An asym/strand identifier corresponding to this gaussian object. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_gaussian_obj_site.asym_id" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_gaussian_obj_site.asym_id" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_gaussian_obj_site.mean_Cartn_x _item_description.description " The mean Cartesian X component corresponding to this gaussian object." # _item.name "_ihm_gaussian_obj_site.mean_Cartn_x" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # loop_ _item_dependent.dependent_name "_ihm_gaussian_obj_site.mean_Cartn_y" "_ihm_gaussian_obj_site.mean_Cartn_z" # save_ # save__ihm_gaussian_obj_site.mean_Cartn_y _item_description.description " The mean Cartesian Y component corresponding to this gaussian object." # _item.name "_ihm_gaussian_obj_site.mean_Cartn_y" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # loop_ _item_dependent.dependent_name "_ihm_gaussian_obj_site.mean_Cartn_x" "_ihm_gaussian_obj_site.mean_Cartn_z" # save_ # save__ihm_gaussian_obj_site.mean_Cartn_z _item_description.description " The mean Cartesian Z component corresponding to this gaussian object." # _item.name "_ihm_gaussian_obj_site.mean_Cartn_z" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # loop_ _item_dependent.dependent_name "_ihm_gaussian_obj_site.mean_Cartn_x" "_ihm_gaussian_obj_site.mean_Cartn_y" # save_ # save__ihm_gaussian_obj_site.weight _item_description.description " The weight of the gaussian object." # _item.name "_ihm_gaussian_obj_site.weight" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_type.code float # save_ # save__ihm_gaussian_obj_site.covariance_matrix[1][1] _item_description.description " Data item [1][1] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_site.covariance_matrix[1][1]" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_site.covariance_matrix[1][2] _item_description.description " Data item [1][2] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_site.covariance_matrix[1][2]" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_site.covariance_matrix[1][3] _item_description.description " Data item [1][3] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_site.covariance_matrix[1][3]" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_site.covariance_matrix[2][1] _item_description.description " Data item [2][1] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_site.covariance_matrix[2][1]" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_site.covariance_matrix[2][2] _item_description.description " Data item [2][2] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_site.covariance_matrix[2][2]" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_site.covariance_matrix[2][3] _item_description.description " Data item [2][3] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_site.covariance_matrix[2][3]" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_site.covariance_matrix[3][1] _item_description.description " Data item [3][1] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_site.covariance_matrix[3][1]" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_site.covariance_matrix[3][2] _item_description.description " Data item [3][2] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_site.covariance_matrix[3][2]" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_site.covariance_matrix[3][3] _item_description.description " Data item [3][3] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_site.covariance_matrix[3][3]" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_site.model_id _item_description.description ; The model id corresponding to the gaussian object. This data item is a pointer to _ihm_model_list.model_id in the IHM_MODEL_LIST category. ; # _item.name "_ihm_gaussian_obj_site.model_id" _item.category_id ihm_gaussian_obj_site _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_gaussian_obj_site.model_id" _item_linked.parent_name "_ihm_model_list.model_id" # save_ # save_ihm_gaussian_obj_ensemble _category.description ; Data items in the IHM_GAUSSIAN_OBJ_ENSEMBLE category records the details of the gaussian objects representing an ensemble or cluster of models. ; _category.id ihm_gaussian_obj_ensemble _category.mandatory_code no # _category_key.name "_ihm_gaussian_obj_ensemble.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_gaussian_obj_ensemble.id _ihm_gaussian_obj_ensemble.entity_id _ihm_gaussian_obj_ensemble.seq_id_begin _ihm_gaussian_obj_ensemble.seq_id_end _ihm_gaussian_obj_ensemble.asym_id _ihm_gaussian_obj_ensemble.mean_Cartn_x _ihm_gaussian_obj_ensemble.mean_Cartn_y _ihm_gaussian_obj_ensemble.mean_Cartn_z _ihm_gaussian_obj_ensemble.weight _ihm_gaussian_obj_ensemble.covariance_matrix[1][1] _ihm_gaussian_obj_ensemble.covariance_matrix[1][2] _ihm_gaussian_obj_ensemble.covariance_matrix[1][3] _ihm_gaussian_obj_ensemble.covariance_matrix[2][1] _ihm_gaussian_obj_ensemble.covariance_matrix[2][2] _ihm_gaussian_obj_ensemble.covariance_matrix[2][3] _ihm_gaussian_obj_ensemble.covariance_matrix[3][1] _ihm_gaussian_obj_ensemble.covariance_matrix[3][2] _ihm_gaussian_obj_ensemble.covariance_matrix[3][3] _ihm_gaussian_obj_ensemble.ensemble_id 1 1 1 6 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 2 1 7 7 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 3 1 8 8 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 4 1 9 9 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 5 1 10 10 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 6 1 11 11 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 7 1 12 12 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 8 1 13 13 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 9 1 14 14 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 10 1 15 15 A 1.0 1.0 1.0 1.0 96.25 0.92 -30.50 0.92 83.82 16.37 -30.50 16.37 95.80 1 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_gaussian_obj_ensemble # save_ # save__ihm_gaussian_obj_ensemble.id _item_description.description " A unique identifier for this gaussian object." # _item.name "_ihm_gaussian_obj_ensemble.id" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_gaussian_obj_ensemble.entity_id _item_description.description ; The entity identifier corresponding to this gaussian object. This data item is a pointer to _entity.id in the ENTITY category. ; # _item.name "_ihm_gaussian_obj_ensemble.entity_id" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_gaussian_obj_ensemble.entity_id" _item_linked.parent_name "_entity.id" # save_ # save__ihm_gaussian_obj_ensemble.seq_id_begin _item_description.description ; The leading sequence index corresponding to this gaussian object. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_gaussian_obj_ensemble.seq_id_begin" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_begin # _item_linked.child_name "_ihm_gaussian_obj_ensemble.seq_id_begin" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_gaussian_obj_ensemble.seq_id_end _item_description.description ; The trailing sequence index corresponding to this gaussian object. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_gaussian_obj_ensemble.seq_id_end" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_end # _item_linked.child_name "_ihm_gaussian_obj_ensemble.seq_id_end" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_gaussian_obj_ensemble.asym_id _item_description.description ; An asym/strand identifier corresponding to this gaussian object. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_gaussian_obj_ensemble.asym_id" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_gaussian_obj_ensemble.asym_id" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_gaussian_obj_ensemble.mean_Cartn_x _item_description.description " The mean Cartesian X component corresponding to this gaussian object." # _item.name "_ihm_gaussian_obj_ensemble.mean_Cartn_x" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # loop_ _item_dependent.dependent_name "_ihm_gaussian_obj_ensemble.mean_Cartn_y" "_ihm_gaussian_obj_ensemble.mean_Cartn_z" # save_ # save__ihm_gaussian_obj_ensemble.mean_Cartn_y _item_description.description " The mean Cartesian Y component corresponding to this gaussian object." # _item.name "_ihm_gaussian_obj_ensemble.mean_Cartn_y" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # loop_ _item_dependent.dependent_name "_ihm_gaussian_obj_ensemble.mean_Cartn_x" "_ihm_gaussian_obj_ensemble.mean_Cartn_z" # save_ # save__ihm_gaussian_obj_ensemble.mean_Cartn_z _item_description.description " The mean Cartesian Z component corresponding to this gaussian object." # _item.name "_ihm_gaussian_obj_ensemble.mean_Cartn_z" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # loop_ _item_dependent.dependent_name "_ihm_gaussian_obj_ensemble.mean_Cartn_x" "_ihm_gaussian_obj_ensemble.mean_Cartn_y" # save_ # save__ihm_gaussian_obj_ensemble.weight _item_description.description " The weight of the gaussian object." # _item.name "_ihm_gaussian_obj_ensemble.weight" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_type.code float # save_ # save__ihm_gaussian_obj_ensemble.covariance_matrix[1][1] _item_description.description " Data item [1][1] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_ensemble.covariance_matrix[1][1]" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_ensemble.covariance_matrix[1][2] _item_description.description " Data item [1][2] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_ensemble.covariance_matrix[1][2]" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_ensemble.covariance_matrix[1][3] _item_description.description " Data item [1][3] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_ensemble.covariance_matrix[1][3]" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_ensemble.covariance_matrix[2][1] _item_description.description " Data item [2][1] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_ensemble.covariance_matrix[2][1]" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_ensemble.covariance_matrix[2][2] _item_description.description " Data item [2][2] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_ensemble.covariance_matrix[2][2]" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_ensemble.covariance_matrix[2][3] _item_description.description " Data item [2][3] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_ensemble.covariance_matrix[2][3]" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_ensemble.covariance_matrix[3][1] _item_description.description " Data item [3][1] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_ensemble.covariance_matrix[3][1]" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_ensemble.covariance_matrix[3][2] _item_description.description " Data item [3][2] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_ensemble.covariance_matrix[3][2]" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_ensemble.covariance_matrix[3][3] _item_description.description " Data item [3][3] of the covariance matrix representing the Gaussian object." # _item.name "_ihm_gaussian_obj_ensemble.covariance_matrix[3][3]" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_gaussian_obj_ensemble.ensemble_id _item_description.description ; The ensemble id corresponding to the gaussian object. This data item is a pointer to _ihm_ensemble_info.ensemble_id in the IHM_ENSEMBLE_INFO category. ; # _item.name "_ihm_gaussian_obj_ensemble.ensemble_id" _item.category_id ihm_gaussian_obj_ensemble _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_gaussian_obj_ensemble.ensemble_id" _item_linked.parent_name "_ihm_ensemble_info.ensemble_id" # save_ # save_ihm_pseudo_site _category.description ; Data items in the IHM_PSEUDO_SITE_FEATURE category records the details of pseudo sites that may be used in the restraints or model representation. ; _category.id ihm_pseudo_site _category.mandatory_code no # _category_key.name "_ihm_pseudo_site.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_pseudo_site.id _ihm_pseudo_site.Cartn_x _ihm_pseudo_site.Cartn_y _ihm_pseudo_site.Cartn_z _ihm_pseudo_site.radius _ihm_pseudo_site.description 1 1.0 1.0 1.0 1.0 . 2 1.0 1.0 1.0 1.0 . 3 1.0 1.0 1.0 1.0 . 4 1.0 1.0 1.0 1.0 . 5 1.0 1.0 1.0 1.0 . # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_pseudo_site # save_ # save__ihm_pseudo_site.id _item_description.description " An identifier to the pseudo site." # _item.name "_ihm_pseudo_site.id" _item.category_id ihm_pseudo_site _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_pseudo_site.Cartn_x _item_description.description " The Cartesian X component corresponding to this pseudo site." # _item.name "_ihm_pseudo_site.Cartn_x" _item.category_id ihm_pseudo_site _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # loop_ _item_dependent.dependent_name "_ihm_pseudo_site.Cartn_y" "_ihm_pseudo_site.Cartn_z" # save_ # save__ihm_pseudo_site.Cartn_y _item_description.description " The Cartesian Y component corresponding to this pseudo site." # _item.name "_ihm_pseudo_site.Cartn_y" _item.category_id ihm_pseudo_site _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # loop_ _item_dependent.dependent_name "_ihm_pseudo_site.Cartn_x" "_ihm_pseudo_site.Cartn_z" # save_ # save__ihm_pseudo_site.Cartn_z _item_description.description " The Cartesian Z component corresponding to this pseudo site." # _item.name "_ihm_pseudo_site.Cartn_z" _item.category_id ihm_pseudo_site _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # loop_ _item_dependent.dependent_name "_ihm_pseudo_site.Cartn_x" "_ihm_pseudo_site.Cartn_y" # save_ # save__ihm_pseudo_site.radius _item_description.description " The radius associated with the pseudo site, if applicable." # _item.name "_ihm_pseudo_site.radius" _item.category_id ihm_pseudo_site _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_pseudo_site.description _item_description.description " Textual description of the pseudo site." # _item.name "_ihm_pseudo_site.description" _item.category_id ihm_pseudo_site _item.mandatory_code no # _item_type.code text # _item_examples.case "centroid of a feature" # save_ # save_ihm_residues_not_modeled _category.description ; Data items in the IHM_RESIDUES_NOT_MODELED category record the details of the residues that are defined in the IHM_STRUCT_ASSEMBLY category but are missing in the three-dimensional model (ATOM_SITE, IHM_SPHERE_OBJ_SITE, IHM_GAUSSIAN_OBJ_SITE categories) i.e., residues in the assembly that are not modeled. ; _category.id ihm_residues_not_modeled _category.mandatory_code no # _category_key.name "_ihm_residues_not_modeled.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 ; _category_examples.case ; loop_ _ihm_residues_not_modeled.id _ihm_residues_not_modeled.model_id _ihm_residues_not_modeled.entity_description _ihm_residues_not_modeled.entity_id _ihm_residues_not_modeled.asym_id _ihm_residues_not_modeled.seq_id_begin _ihm_residues_not_modeled.seq_id_end _ihm_residues_not_modeled.comp_id_begin _ihm_residues_not_modeled.comp_id_end _ihm_residues_not_modeled.reason 1 1 Nup84 1 A 1 14 MET LYS 'Highly variable models with poor precision' 2 1 Nup85 2 B 740 744 ALA MET 'Highly variable models with poor precision' 3 1 Nup133 4 D 5 26 LYS LEU 'Highly variable models with poor precision' 4 1 Nup145 5 E 707 712 LYS ILE 'Highly variable models with poor precision' #...abbreviated... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_residues_not_modeled # save_ # save__ihm_residues_not_modeled.id _item_description.description " A unique identifier for the category." # _item.name "_ihm_residues_not_modeled.id" _item.category_id ihm_residues_not_modeled _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_residues_not_modeled.model_id _item_description.description ; An identifier for the structural model. This data item is a pointer to _ihm_model_list.model_id in the IHM_MODEL_LIST category. ; # _item.name "_ihm_residues_not_modeled.model_id" _item.category_id ihm_residues_not_modeled _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_residues_not_modeled.model_id" _item_linked.parent_name "_ihm_model_list.model_id" # save_ # save__ihm_residues_not_modeled.entity_description _item_description.description ; A text description of the molecular entity, whose residues are not modeled. This data item is a pointer to _entity.pdbx_description in the ENTITY category. ; # _item.name "_ihm_residues_not_modeled.entity_description" _item.category_id ihm_residues_not_modeled _item.mandatory_code no # _item_type.code line # save_ # save__ihm_residues_not_modeled.entity_id _item_description.description ; A unique identifier to the molecular entity, whose residues are not modeled. This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_residues_not_modeled.entity_id" _item.category_id ihm_residues_not_modeled _item.mandatory_code yes # _item_type.code code # loop_ _item_sub_category.id _item_sub_category.pdbx_label mm_poly_res_label mm_poly_res_label_begin mm_poly_res_label mm_poly_res_label_end # _item_linked.child_name "_ihm_residues_not_modeled.entity_id" _item_linked.parent_name "_entity_poly_seq.entity_id" # save_ # save__ihm_residues_not_modeled.asym_id _item_description.description ; An asym/strand identifier. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_residues_not_modeled.asym_id" _item.category_id ihm_residues_not_modeled _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_residues_not_modeled.asym_id" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_residues_not_modeled.seq_id_begin _item_description.description ; The starting residue index for the sequence segment of missing residues. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_residues_not_modeled.seq_id_begin" _item.category_id ihm_residues_not_modeled _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_begin # _item_linked.child_name "_ihm_residues_not_modeled.seq_id_begin" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_residues_not_modeled.seq_id_end _item_description.description ; The ending residue index for the sequence segment of missing residues. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_residues_not_modeled.seq_id_end" _item.category_id ihm_residues_not_modeled _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_end # _item_linked.child_name "_ihm_residues_not_modeled.seq_id_end" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_residues_not_modeled.comp_id_begin _item_description.description ; The starting residue for the sequence segment of missing residues. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_residues_not_modeled.comp_id_begin" _item.category_id ihm_residues_not_modeled _item.mandatory_code yes # _item_type.code ucode # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_begin # _item_linked.child_name "_ihm_residues_not_modeled.comp_id_begin" _item_linked.parent_name "_entity_poly_seq.mon_id" # save_ # save__ihm_residues_not_modeled.comp_id_end _item_description.description ; The ending residue for the sequence segment of missing residues. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_residues_not_modeled.comp_id_end" _item.category_id ihm_residues_not_modeled _item.mandatory_code yes # _item_type.code ucode # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_end # _item_linked.child_name "_ihm_residues_not_modeled.comp_id_end" _item_linked.parent_name "_entity_poly_seq.mon_id" # save_ # save__ihm_residues_not_modeled.reason _item_description.description " The reason why the residues are missing in the structural model." # _item.name "_ihm_residues_not_modeled.reason" _item.category_id ihm_residues_not_modeled _item.mandatory_code no # _item_type.code line # loop_ _item_enumeration.value "Highly variable models with poor precision" "Models do not adequately satisfy input data" Other # save_ # save__ihm_residues_not_modeled.details _item_description.description " Additional details regarding the missing segments." # _item.name "_ihm_residues_not_modeled.details" _item.category_id ihm_residues_not_modeled _item.mandatory_code no # _item_type.code text # save_ # save_ihm_feature_list _category.description ; IHM_FEATURE_LIST is the high level category that provides defintions to select atoms/residues from polymeric and non-polymeric entities. ; _category.id ihm_feature_list _category.mandatory_code no # _category_key.name "_ihm_feature_list.feature_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_feature_list.feature_id _ihm_feature_list.feature_type _ihm_feature_list.entity_type 1 atom polymer 2 residue polymer 3 atom non-polymer # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_feature_list # save_ # save__ihm_feature_list.feature_id _item_description.description " A unique identifier for the feature." # _item.name "_ihm_feature_list.feature_id" _item.category_id ihm_feature_list _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_feature_list.feature_type _item_description.description " The type of feature." # _item.name "_ihm_feature_list.feature_type" _item.category_id ihm_feature_list _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail atom "feature is an atom or a set of atoms from a polymeric or non-polymeric entity" residue "feature is a residue or a set of residues from a polymeric entity, each represented by the alpha carbon atom" "residue range" "feature is a set of residues in a contiguous range from a polymeric entity, each represented by the alpha carbon atom" ligand "feature is an instance or a set of instances of non-polymeric entities" "pseudo site" "feature is a pseudo site" # save_ # save__ihm_feature_list.entity_type _item_description.description " The type of entity." # _item.name "_ihm_feature_list.entity_type" _item.category_id ihm_feature_list _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value polymer non-polymer water other # save_ # save__ihm_feature_list.details _item_description.description " Additional details regarding the feature." # _item.name "_ihm_feature_list.details" _item.category_id ihm_feature_list _item.mandatory_code no # _item_type.code text # save_ # save_ihm_pseudo_site_feature _category.description ; Data items in the IHM_PSEUDO_SITE_FEATURE category records the details of pseudo site features listed in IHM_FEATURE_LIST. ; _category.id ihm_pseudo_site_feature _category.mandatory_code no # _category_key.name "_ihm_pseudo_site_feature.feature_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_pseudo_site_feature.feature_id _ihm_pseudo_site_feature.pseudo_site_id 1 1 2 2 3 3 4 4 5 5 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_pseudo_site_feature # save_ # save__ihm_pseudo_site_feature.feature_id _item_description.description ; The feature identifier corresponding to this pseudo site. This data item is a pointer to _ihm_feature_list.feature_id in the IHM_FEATURE_LIST category. ; # _item.name "_ihm_pseudo_site_feature.feature_id" _item.category_id ihm_pseudo_site_feature _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_pseudo_site_feature.feature_id" _item_linked.parent_name "_ihm_feature_list.feature_id" # save_ # save__ihm_pseudo_site_feature.pseudo_site_id _item_description.description ; The pseudo site identifier corresponding to this feature. This data item is a pointer to _ihm_pseudo_site.id in the IHM_PSEUDO_SITE category. ; # _item.name "_ihm_pseudo_site_feature.pseudo_site_id" _item.category_id ihm_pseudo_site_feature _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_pseudo_site_feature.pseudo_site_id" _item_linked.parent_name "_ihm_pseudo_site.id" # save_ # save_ihm_poly_atom_feature _category.description ; Data items in the IHM_POLY_ATOM_FEATURE category provides the defintions required to select specific atoms. ; _category.id ihm_poly_atom_feature _category.mandatory_code no # _category_key.name "_ihm_poly_atom_feature.ordinal_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_poly_atom_feature.ordinal_id _ihm_poly_atom_feature.feature_id _ihm_poly_atom_feature.entity_id _ihm_poly_atom_feature.asym_id _ihm_poly_atom_feature.seq_id _ihm_poly_atom_feature.comp_id _ihm_poly_atom_feature.atom_id 1 1 3 C 17 LYS CB 2 2 3 C 206 LYS CB 3 3 3 C 38 LYS CB 4 4 3 C 400 LYS CB 5 5 3 C 400 LYS CB 6 6 3 C 400 LYS CB 7 7 3 C 735 LYS CB 8 8 3 C 735 LYS CB 9 9 3 C 865 LYS CB 10 10 3 C 865 LYS CB 11 11 4 D 103 LYS CB 12 12 4 D 103 LYS CB # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_poly_atom_feature # save_ # save__ihm_poly_atom_feature.ordinal_id _item_description.description " A unique identifier for the category." # _item.name "_ihm_poly_atom_feature.ordinal_id" _item.category_id ihm_poly_atom_feature _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_poly_atom_feature.feature_id _item_description.description ; An identifier for the selected atom feature. This data item is a pointer to _ihm_feature_list.feature_id in the IHM_FEATURE_LIST category. ; # _item.name "_ihm_poly_atom_feature.feature_id" _item.category_id ihm_poly_atom_feature _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_poly_atom_feature.feature_id" _item_linked.parent_name "_ihm_feature_list.feature_id" # save_ # save__ihm_poly_atom_feature.entity_id _item_description.description ; The entity identifier of the atom. This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_poly_atom_feature.entity_id" _item.category_id ihm_poly_atom_feature _item.mandatory_code yes # _item_type.code code # _item_sub_category.id mm_poly_res_label # _item_linked.child_name "_ihm_poly_atom_feature.entity_id" _item_linked.parent_name "_entity_poly_seq.entity_id" # save_ # save__ihm_poly_atom_feature.asym_id _item_description.description ; An asym/strand identifier of the atom, if applicable. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_poly_atom_feature.asym_id" _item.category_id ihm_poly_atom_feature _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_ihm_poly_atom_feature.asym_id" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_poly_atom_feature.comp_id _item_description.description ; The component identifier of the atom. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_poly_atom_feature.comp_id" _item.category_id ihm_poly_atom_feature _item.mandatory_code yes # _item_type.code ucode # _item_sub_category.id mm_poly_res_label # _item_linked.child_name "_ihm_poly_atom_feature.comp_id" _item_linked.parent_name "_entity_poly_seq.mon_id" # save_ # save__ihm_poly_atom_feature.seq_id _item_description.description ; The sequence index of the residue to which the atom belongs. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_poly_atom_feature.seq_id" _item.category_id ihm_poly_atom_feature _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label # _item_linked.child_name "_ihm_poly_atom_feature.seq_id" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_poly_atom_feature.atom_id _item_description.description ; The identifier of the atom. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; # _item.name "_ihm_poly_atom_feature.atom_id" _item.category_id ihm_poly_atom_feature _item.mandatory_code no # _item_type.code atcode # _item_linked.child_name "_ihm_poly_atom_feature.atom_id" _item_linked.parent_name "_chem_comp_atom.atom_id" # save_ # save_ihm_poly_residue_feature _category.description ; Data items in the IHM_POLY_RESIDUE_FEATURE category provides the defintions required to select a specific residue or a set of residues that may or may not be in a contiguous range. ; _category.id ihm_poly_residue_feature _category.mandatory_code no # _category_key.name "_ihm_poly_residue_feature.ordinal_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_poly_residue_feature.ordinal_id _ihm_poly_residue_feature.feature_id _ihm_poly_residue_feature.entity_id _ihm_poly_residue_feature.asym_id _ihm_poly_residue_feature.seq_id_begin _ihm_poly_residue_feature.comp_id_begin _ihm_poly_residue_feature.seq_id_end _ihm_poly_residue_feature.comp_id_end _ihm_poly_residue_feature.interface_residue_flag 1 1 3 C 17 LYS 17 LYS NO # Single residue selection 2 2 3 C 206 LYS 206 LYS NO 3 3 3 C 38 THR 54 ALA NO # Residue range selection 4 4 3 C 400 LEU 428 PHE NO 5 5 3 C 429 GLN 429 GLN NO 6 6 3 C 461 LEU 478 ARG NO 7 7 3 C 735 ASP 735 ASP NO 8 8 3 C 865 SER 891 VAL NO # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_poly_residue_feature # save_ # save__ihm_poly_residue_feature.ordinal_id _item_description.description " A unique identifier for the category." # _item.name "_ihm_poly_residue_feature.ordinal_id" _item.category_id ihm_poly_residue_feature _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_poly_residue_feature.feature_id _item_description.description ; An identifier for the selected residue / residue range feature. This data item is a pointer to _ihm_feature_list.feature_id in the IHM_FEATURE_LIST category. ; # _item.name "_ihm_poly_residue_feature.feature_id" _item.category_id ihm_poly_residue_feature _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_poly_residue_feature.feature_id" _item_linked.parent_name "_ihm_feature_list.feature_id" # save_ # save__ihm_poly_residue_feature.entity_id _item_description.description ; The entity identifier for residue / residue range. This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_poly_residue_feature.entity_id" _item.category_id ihm_poly_residue_feature _item.mandatory_code yes # _item_type.code code # loop_ _item_sub_category.id _item_sub_category.pdbx_label mm_poly_res_label mm_poly_res_label_begin mm_poly_res_label mm_poly_res_label_end # _item_linked.child_name "_ihm_poly_residue_feature.entity_id" _item_linked.parent_name "_entity_poly_seq.entity_id" # save_ # save__ihm_poly_residue_feature.asym_id _item_description.description ; An asym/strand identifier for the residue / residue range, if applicable. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_poly_residue_feature.asym_id" _item.category_id ihm_poly_residue_feature _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_ihm_poly_residue_feature.asym_id" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_poly_residue_feature.comp_id_begin _item_description.description ; The component identifier of the beginning residue / residue range. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_poly_residue_feature.comp_id_begin" _item.category_id ihm_poly_residue_feature _item.mandatory_code no # _item_type.code ucode # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_begin # _item_linked.child_name "_ihm_poly_residue_feature.comp_id_begin" _item_linked.parent_name "_entity_poly_seq.mon_id" # save_ # save__ihm_poly_residue_feature.comp_id_end _item_description.description ; The component identifier of the ending residue / residue range. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_poly_residue_feature.comp_id_end" _item.category_id ihm_poly_residue_feature _item.mandatory_code no # _item_type.code ucode # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_end # _item_linked.child_name "_ihm_poly_residue_feature.comp_id_end" _item_linked.parent_name "_entity_poly_seq.mon_id" # save_ # save__ihm_poly_residue_feature.seq_id_begin _item_description.description ; The sequence index of the beginning residue / residue range. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_poly_residue_feature.seq_id_begin" _item.category_id ihm_poly_residue_feature _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_begin # _item_linked.child_name "_ihm_poly_residue_feature.seq_id_begin" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_poly_residue_feature.seq_id_end _item_description.description ; The sequence index of the ending residue / residue range. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; # _item.name "_ihm_poly_residue_feature.seq_id_end" _item.category_id ihm_poly_residue_feature _item.mandatory_code yes # _item_type.code int # _item_sub_category.id mm_poly_res_label _item_sub_category.pdbx_label mm_poly_res_label_end # _item_linked.child_name "_ihm_poly_residue_feature.seq_id_end" _item_linked.parent_name "_entity_poly_seq.num" # save_ # save__ihm_poly_residue_feature.residue_range_granularity _item_description.description " The coarse-graining information, if the feature is a residue range." # _item.name "_ihm_poly_residue_feature.residue_range_granularity" _item.category_id ihm_poly_residue_feature _item.mandatory_code no # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail by-residue "Residue range represented by individual residues in the residue range" by-feature "Residue range represented using the closest primitive object with the highest resolution" # save_ # save__ihm_poly_residue_feature.rep_atom _item_description.description ; If _ihm_poly_residue_feature.granularity is by-residue, then indicate the atom used to represent the residue in three-dimension. Default is the C-alpha atom. ; # _item.name "_ihm_poly_residue_feature.rep_atom" _item.category_id ihm_poly_residue_feature _item.mandatory_code no # _item_type.code code # _item_default.value CA # loop_ _item_enumeration.value _item_enumeration.detail CA "C-alpha for all residues" CB "C-beta for all residues except Glycine; Default value of C-alpha for Glycine" # save_ # save__ihm_poly_residue_feature.interface_residue_flag _item_description.description ; A flag to indicate if the feature is an interface residue, identified by experiments and therefore, used to build spatial restraints during modeling. ; # _item.name "_ihm_poly_residue_feature.interface_residue_flag" _item.category_id ihm_poly_residue_feature _item.mandatory_code no # _item_type.code ucode # loop_ _item_enumeration.value _item_enumeration.detail YES . NO . # save_ # save_ihm_non_poly_feature _category.description ; Data items in the IHM_NON_POLY_FEATURE category provides the defintions required to select a non-polymeric (ligand) feature. ; _category.id ihm_non_poly_feature _category.mandatory_code no # _category_key.name "_ihm_non_poly_feature.ordinal_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_non_poly_feature.ordinal_id _ihm_non_poly_feature.feature_id _ihm_non_poly_feature.entity_id _ihm_non_poly_feature.asym_id _ihm_non_poly_feature.comp_id _ihm_non_poly_feature.atom_id 1 1 6 F FES FE1 2 2 6 F FES FE2 3 3 6 F FES S1 4 4 6 F FES S2 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_non_poly_feature # save_ # save__ihm_non_poly_feature.ordinal_id _item_description.description " A unique identifier for the category." # _item.name "_ihm_non_poly_feature.ordinal_id" _item.category_id ihm_non_poly_feature _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_non_poly_feature.feature_id _item_description.description ; An identifier for the selected non-polymer feature. This data item is a pointer to _ihm_feature_list.feature_id in the IHM_FEATURE_LIST category. ; # _item.name "_ihm_non_poly_feature.feature_id" _item.category_id ihm_non_poly_feature _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_non_poly_feature.feature_id" _item_linked.parent_name "_ihm_feature_list.feature_id" # save_ # save__ihm_non_poly_feature.entity_id _item_description.description ; The entity identifier of the non-polymer feature. This data item is a pointer to _entity.id in the ENTITY category. ; # _item.name "_ihm_non_poly_feature.entity_id" _item.category_id ihm_non_poly_feature _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_non_poly_feature.entity_id" _item_linked.parent_name "_entity.id" # save_ # save__ihm_non_poly_feature.asym_id _item_description.description ; An asym/strand identifier of the non-polymer feature, if applicable. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_non_poly_feature.asym_id" _item.category_id ihm_non_poly_feature _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_ihm_non_poly_feature.asym_id" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_non_poly_feature.comp_id _item_description.description ; The component identifier of the non-polymer feature. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; # _item.name "_ihm_non_poly_feature.comp_id" _item.category_id ihm_non_poly_feature _item.mandatory_code yes # _item_type.code ucode # _item_linked.child_name "_ihm_non_poly_feature.comp_id" _item_linked.parent_name "_chem_comp.id" # save_ # save__ihm_non_poly_feature.atom_id _item_description.description ; The identifier of the non-polymeric atom, if applicable. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; # _item.name "_ihm_non_poly_feature.atom_id" _item.category_id ihm_non_poly_feature _item.mandatory_code no # _item_type.code atcode # _item_linked.child_name "_ihm_non_poly_feature.atom_id" _item_linked.parent_name "_chem_comp_atom.atom_id" # save_ # save_ihm_interface_residue_feature _category.description ; Data items in the IHM_INTERFACE_RESIDUE_FEATURE category captures the details of residues that are identified to be at the binding interface from experiments. This information is used by modeling software such as HADDOCK to create a set of ambiguous distance restraints at the binding interface between the molecular entities involved. ; _category.id ihm_interface_residue_feature _category.mandatory_code no # _category_key.name "_ihm_interface_residue_feature.ordinal_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_interface_residue_feature.ordinal_id _ihm_interface_residue_feature.feature_id _ihm_interface_residue_feature.binding_partner_entity_id _ihm_interface_residue_feature.binding_partner_asym_id _ihm_interface_residue_feature.dataset_list_id _ihm_interface_residue_feature.details 1 1 2 B 5 . 2 2 2 B 5 . 3 3 2 B 5 . 4 4 2 B 5 . 5 5 1 A 4 . 6 6 1 A 4 . 7 7 1 A 4 . 8 8 1 A 4 . 9 9 1 A 4 . # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_interface_residue_feature # save_ # save__ihm_interface_residue_feature.ordinal_id _item_description.description " A unique identifier for the category." # _item.name "_ihm_interface_residue_feature.ordinal_id" _item.category_id ihm_interface_residue_feature _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_interface_residue_feature.feature_id _item_description.description ; Identifier for the interface residue feature that defines the interface residue. This data item is a pointer to _ihm_feature_list.feature_id in the IHM_FEATURE_LIST category. ; # _item.name "_ihm_interface_residue_feature.feature_id" _item.category_id ihm_interface_residue_feature _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_interface_residue_feature.feature_id" _item_linked.parent_name "_ihm_feature_list.feature_id" # save_ # save__ihm_interface_residue_feature.binding_partner_entity_id _item_description.description ; The entity identifier of the binding partner at the interface. This data item is a pointer to _entity.id in the ENTITY category. ; # _item.name "_ihm_interface_residue_feature.binding_partner_entity_id" _item.category_id ihm_interface_residue_feature _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_interface_residue_feature.binding_partner_entity_id" _item_linked.parent_name "_entity.id" # save_ # save__ihm_interface_residue_feature.binding_partner_asym_id _item_description.description ; An asym/strand identifier for the binding partner at the interface, if applicable. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; # _item.name "_ihm_interface_residue_feature.binding_partner_asym_id" _item.category_id ihm_interface_residue_feature _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_ihm_interface_residue_feature.binding_partner_asym_id" _item_linked.parent_name "_struct_asym.id" # save_ # save__ihm_interface_residue_feature.dataset_list_id _item_description.description ; Identifier to the input data from which the interface residue is determined. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_interface_residue_feature.dataset_list_id" _item.category_id ihm_interface_residue_feature _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_interface_residue_feature.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save__ihm_interface_residue_feature.details _item_description.description " Additional details regarding the interface residue." # _item.name "_ihm_interface_residue_feature.details" _item.category_id ihm_interface_residue_feature _item.mandatory_code no # _item_type.code text # save_ # save_ihm_derived_distance_restraint _category.description ; Data items in the IHM_DERIVED_DISTANCE_RESTRAINT category records the list of distance restraints used in the integrative modeling experiment. These distance redistance restraints may be derived from various kinds of experiments. ; _category.id ihm_derived_distance_restraint _category.mandatory_code no # _category_key.name "_ihm_derived_distance_restraint.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_derived_distance_restraint.id _ihm_derived_distance_restraint.feature_id_1 _ihm_derived_distance_restraint.feature_id_2 _ihm_derived_distance_restraint.restraint_type _ihm_derived_distance_restraint.distance_upper_limit _ihm_derived_distance_restraint.probability _ihm_derived_distance_restraint.dataset_list_id 1 7 21 'upper bound' 8.0 0.8 1 2 16 19 'upper bound' 8.0 0.5 1 3 8 40 'upper bound' 8.0 0.8 1 4 35 43 'upper bound' 8.0 0.6 1 5 23 45 'upper bound' 8.0 0.7 1 6 86 94 'upper bound' 8.0 0.7 1 7 63 80 'upper bound' 8.0 0.5 1 8 15 33 'upper bound' 8.0 0.5 1 9 41 52 'upper bound' 8.0 0.9 1 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_derived_distance_restraint # save_ # save__ihm_derived_distance_restraint.id _item_description.description " A unique identifier for the derived distance restraint." # _item.name "_ihm_derived_distance_restraint.id" _item.category_id ihm_derived_distance_restraint _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_derived_distance_restraint.group_id _item_description.description ; An identifier to group the distance restraints. This can be the same as the _ihm_derived_distance_restraint.id in case the some of the restraints are not grouped. ; # _item.name "_ihm_derived_distance_restraint.group_id" _item.category_id ihm_derived_distance_restraint _item.mandatory_code no # _item_type.code int # save_ # save__ihm_derived_distance_restraint.feature_id_1 _item_description.description ; The feature identifier for the first partner in the distance restraint. This data item is a pointer to _ihm_feature_list.feature_id in the IHM_FEATURE_LIST category. ; # _item.name "_ihm_derived_distance_restraint.feature_id_1" _item.category_id ihm_derived_distance_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_derived_distance_restraint.feature_id_1" _item_linked.parent_name "_ihm_feature_list.feature_id" # save_ # save__ihm_derived_distance_restraint.feature_id_2 _item_description.description ; The feature identifier for the second partner in the distance restraint. This data item is a pointer to _ihm_feature_list.feature_id in the IHM_FEATURE_LIST category. ; # _item.name "_ihm_derived_distance_restraint.feature_id_2" _item.category_id ihm_derived_distance_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_derived_distance_restraint.feature_id_2" _item_linked.parent_name "_ihm_feature_list.feature_id" # save_ # save__ihm_derived_distance_restraint.group_conditionality _item_description.description ; If a group of atoms or residues are restrained, this data item defines the conditionality based on which the restraint is applied in the modeling. ; # _item.name "_ihm_derived_distance_restraint.group_conditionality" _item.category_id ihm_derived_distance_restraint _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail ALL "All distances among the group of atoms or residues are restrained" ANY "Any one of the distances among the group of atoms or residues could be satisfied" # save_ # save__ihm_derived_distance_restraint.random_exclusion_fraction _item_description.description ; The fraction of randomly excluded distance restraints during modeling. In HADDOCK, this is used along with ambiguous interface restraints (AIRs) to account for uncertainties in AIRs. ; # _item.name "_ihm_derived_distance_restraint.random_exclusion_fraction" _item.category_id ihm_derived_distance_restraint _item.mandatory_code no # _item_type.code float # save_ # save__ihm_derived_distance_restraint.distance_lower_limit _item_description.description ; The lower limit to the distance threshold applied to this distance restraint in the integrative modeling task. ; # _item.name "_ihm_derived_distance_restraint.distance_lower_limit" _item.category_id ihm_derived_distance_restraint _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_derived_distance_restraint.distance_upper_limit _item_description.description ; The upper limit to the distance threshold applied to this distance restraint in the integrative modeling task. ; # _item.name "_ihm_derived_distance_restraint.distance_upper_limit" _item.category_id ihm_derived_distance_restraint _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_derived_distance_restraint.distance_lower_limit_esd _item_description.description ; The estimated standard deviation of the lower limit distance threshold applied to this distance restraint in the integrative modeling task. ; # _item.name "_ihm_derived_distance_restraint.distance_lower_limit_esd" _item.category_id ihm_derived_distance_restraint _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_derived_distance_restraint.distance_upper_limit_esd _item_description.description ; The estimated standard deviation of the upper limit distance threshold applied to this distance restraint in the integrative modeling task. ; # _item.name "_ihm_derived_distance_restraint.distance_upper_limit_esd" _item.category_id ihm_derived_distance_restraint _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_derived_distance_restraint.probability _item_description.description ; The real number that indicates the probability that the distance restraint is correct. This number should fall between 0.0 and 1.0. ; # _item.name "_ihm_derived_distance_restraint.probability" _item.category_id ihm_derived_distance_restraint _item.mandatory_code no # _item_type.code float # loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 1.0 1.0 1.0 # save_ # save__ihm_derived_distance_restraint.restraint_type _item_description.description " The type of distance restraint applied." # _item.name "_ihm_derived_distance_restraint.restraint_type" _item.category_id ihm_derived_distance_restraint _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value "lower bound" "upper bound" "lower and upper bound" harmonic # save_ # save__ihm_derived_distance_restraint.mic_value _item_description.description ; The value of the Maximal Information Co-efficient (MIC), if applicable. MIC values are correlation measures derived from the genetic profiles and are used to derive restraint information from quantitative measurements of genetic interactions. ; # _item.name "_ihm_derived_distance_restraint.mic_value" _item.category_id ihm_derived_distance_restraint _item.mandatory_code no # _item_type.code float # save_ # save__ihm_derived_distance_restraint.distance_threshold_mean _item_description.description " The distance threshold mean applied to the restraint." # _item.name "_ihm_derived_distance_restraint.distance_threshold_mean" _item.category_id ihm_derived_distance_restraint _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_derived_distance_restraint.distance_threshold_esd _item_description.description " The estimated standard deviation of the distance threshold applied to the restraint." # _item.name "_ihm_derived_distance_restraint.distance_threshold_esd" _item.category_id ihm_derived_distance_restraint _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_derived_distance_restraint.dataset_list_id _item_description.description ; Identifier to the input data from which the distance restraint is derived. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category. This data item may not be applicable for all cases. For example, in case of ambiguous interface restraints where the interface residues are identified from multiple experiments, the reference to the _ihm_dataset_list.id is handled in the IHM_INTERFACE_RESIDUE_FEATURE category rather than here. ; # _item.name "_ihm_derived_distance_restraint.dataset_list_id" _item.category_id ihm_derived_distance_restraint _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_derived_distance_restraint.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save_ihm_derived_angle_restraint _category.description ; Data items in the IHM_DERIVED_ANGLE_RESTRAINT category records the list of angle restraints used in the integrative modeling experiment. These angle restraints may be derived from various kinds of experiments. ; _category.id ihm_derived_angle_restraint _category.mandatory_code no # _category_key.name "_ihm_derived_angle_restraint.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_derived_angle_restraint.id _ihm_derived_angle_restraint.feature_id_1 _ihm_derived_angle_restraint.feature_id_2 _ihm_derived_angle_restraint.feature_id_3 _ihm_derived_angle_restraint.restraint_type _ihm_derived_angle_restraint.harmonic_angle_threshold_mean _ihm_derived_angle_restraint.harmonic_angle_threshold_esd _ihm_derived_angle_restraint.dataset_list_id 1 9 17 1 'harmonic' 114.6 1.0 5 2 10 18 2 'harmonic' 116.9 1.0 5 3 11 19 3 'harmonic' 112.9 1.0 5 4 12 20 4 'harmonic' 108.9 1.0 5 5 13 21 5 'harmonic' 114.6 1.0 5 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_derived_angle_restraint # save_ # save__ihm_derived_angle_restraint.id _item_description.description " A unique identifier for the derived angle restraint." # _item.name "_ihm_derived_angle_restraint.id" _item.category_id ihm_derived_angle_restraint _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_derived_angle_restraint.group_id _item_description.description ; An identifier to group the angle restraints. This can be the same as the _ihm_derived_angle_restraint.id in case the restraints are not grouped. ; # _item.name "_ihm_derived_angle_restraint.group_id" _item.category_id ihm_derived_angle_restraint _item.mandatory_code no # _item_type.code int # save_ # save__ihm_derived_angle_restraint.feature_id_1 _item_description.description ; The feature identifier for the first partner in the angle restraint. This data item is a pointer to _ihm_feature_list.feature_id in the IHM_FEATURE_LIST category. ; # _item.name "_ihm_derived_angle_restraint.feature_id_1" _item.category_id ihm_derived_angle_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_derived_angle_restraint.feature_id_1" _item_linked.parent_name "_ihm_feature_list.feature_id" # save_ # save__ihm_derived_angle_restraint.feature_id_2 _item_description.description ; The feature identifier for the second partner in the angle restraint. This data item is a pointer to _ihm_feature_list.feature_id in the IHM_FEATURE_LIST category. ; # _item.name "_ihm_derived_angle_restraint.feature_id_2" _item.category_id ihm_derived_angle_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_derived_angle_restraint.feature_id_2" _item_linked.parent_name "_ihm_feature_list.feature_id" # save_ # save__ihm_derived_angle_restraint.feature_id_3 _item_description.description ; The feature identifier for the third partner in the angle restraint. This data item is a pointer to _ihm_feature_list.feature_id in the IHM_FEATURE_LIST category. ; # _item.name "_ihm_derived_angle_restraint.feature_id_3" _item.category_id ihm_derived_angle_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_derived_angle_restraint.feature_id_3" _item_linked.parent_name "_ihm_feature_list.feature_id" # save_ # save__ihm_derived_angle_restraint.group_conditionality _item_description.description ; If a group of angles are restrained together, this data item defines the conditionality based on which the restraint is applied in the modeling. ; # _item.name "_ihm_derived_angle_restraint.group_conditionality" _item.category_id ihm_derived_angle_restraint _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail ALL "All angles in the group are required to be satisfied" ANY "Any one of the angles in the group could be satisfied" # save_ # save__ihm_derived_angle_restraint.angle_lower_limit _item_description.description ; The lower limit to the threshold applied to this angle restraint in the integrative modeling task. ; # _item.name "_ihm_derived_angle_restraint.angle_lower_limit" _item.category_id ihm_derived_angle_restraint _item.mandatory_code no # _item_type.code float # _item_units.code degrees # save_ # save__ihm_derived_angle_restraint.angle_upper_limit _item_description.description ; The upper limit to the threshold applied to this angle restraint in the integrative modeling task. ; # _item.name "_ihm_derived_angle_restraint.angle_upper_limit" _item.category_id ihm_derived_angle_restraint _item.mandatory_code no # _item_type.code float # _item_units.code degrees # save_ # save__ihm_derived_angle_restraint.angle_lower_limit_esd _item_description.description " The estimated standard deviation of the lower limit angle threshold applied." # _item.name "_ihm_derived_angle_restraint.angle_lower_limit_esd" _item.category_id ihm_derived_angle_restraint _item.mandatory_code no # _item_type.code float # _item_units.code degrees # save_ # save__ihm_derived_angle_restraint.angle_upper_limit_esd _item_description.description " The estimated standard deviation of the upper limit angle threshold applied." # _item.name "_ihm_derived_angle_restraint.angle_upper_limit_esd" _item.category_id ihm_derived_angle_restraint _item.mandatory_code no # _item_type.code float # _item_units.code degrees # save_ # save__ihm_derived_angle_restraint.probability _item_description.description ; The real number that indicates the probability that the angle restraint is correct. This number should fall between 0.0 and 1.0. ; # _item.name "_ihm_derived_angle_restraint.probability" _item.category_id ihm_derived_angle_restraint _item.mandatory_code no # _item_type.code float # loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 1.0 1.0 1.0 # save_ # save__ihm_derived_angle_restraint.restraint_type _item_description.description " The type of angle restraint applied." # _item.name "_ihm_derived_angle_restraint.restraint_type" _item.category_id ihm_derived_angle_restraint _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value "lower bound" "upper bound" "lower and upper bound" harmonic # save_ # save__ihm_derived_angle_restraint.angle_threshold_mean _item_description.description " The angle threshold mean applied to the restraint." # _item.name "_ihm_derived_angle_restraint.angle_threshold_mean" _item.category_id ihm_derived_angle_restraint _item.mandatory_code no # _item_type.code float # _item_units.code degrees # save_ # save__ihm_derived_angle_restraint.angle_threshold_esd _item_description.description " The estimated standard deviation of the angle threshold applied to the restraint." # _item.name "_ihm_derived_angle_restraint.angle_threshold_esd" _item.category_id ihm_derived_angle_restraint _item.mandatory_code no # _item_type.code float # _item_units.code degrees # save_ # save__ihm_derived_angle_restraint.dataset_list_id _item_description.description ; Identifier to the input data from which the angle restraint is derived. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_derived_angle_restraint.dataset_list_id" _item.category_id ihm_derived_angle_restraint _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_derived_angle_restraint.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save_ihm_derived_dihedral_restraint _category.description ; Data items in the IHM_DERIVED_DIHEDRAL_RESTRAINT category records the list of dihedral restraints used in the integrative modeling experiment. These dihedral restraints may be derived from various kinds of experiments. ; _category.id ihm_derived_dihedral_restraint _category.mandatory_code no # _category_key.name "_ihm_derived_dihedral_restraint.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_derived_dihedral_restraint.id _ihm_derived_dihedral_restraint.feature_id_1 _ihm_derived_dihedral_restraint.feature_id_2 _ihm_derived_dihedral_restraint.feature_id_3 _ihm_derived_dihedral_restraint.feature_id_4 _ihm_derived_dihedral_restraint.restraint_type _ihm_derived_dihedral_restraint.harmonic_dihedral_threshold_mean _ihm_derived_dihedral_restraint.harmonic_dihedral_threshold_esd _ihm_derived_dihedral_restraint.dataset_list_id 1 25 9 17 1 'harmonic' 56.1 2.3 6 2 26 10 18 2 'harmonic' -52.7 2.3 6 3 27 11 19 3 'harmonic' -71.6 2.3 6 4 28 12 20 4 'harmonic' 58.4 2.3 6 5 29 13 21 5 'harmonic' 56.1 2.3 6 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_derived_dihedral_restraint # save_ # save__ihm_derived_dihedral_restraint.id _item_description.description " A unique identifier for the derived dihedral restraint." # _item.name "_ihm_derived_dihedral_restraint.id" _item.category_id ihm_derived_dihedral_restraint _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_derived_dihedral_restraint.group_id _item_description.description ; An identifier to group the dihedral restraints. This can be the same as the _ihm_derived_dihedral_restraint.id in case the restraints are not grouped. ; # _item.name "_ihm_derived_dihedral_restraint.group_id" _item.category_id ihm_derived_dihedral_restraint _item.mandatory_code no # _item_type.code int # save_ # save__ihm_derived_dihedral_restraint.feature_id_1 _item_description.description ; The feature identifier for the first partner in the dihedral restraint. This data item is a pointer to _ihm_feature_list.feature_id in the IHM_FEATURE_LIST category. ; # _item.name "_ihm_derived_dihedral_restraint.feature_id_1" _item.category_id ihm_derived_dihedral_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_derived_dihedral_restraint.feature_id_1" _item_linked.parent_name "_ihm_feature_list.feature_id" # save_ # save__ihm_derived_dihedral_restraint.feature_id_2 _item_description.description ; The feature identifier for the second partner in the dihedral restraint. This data item is a pointer to _ihm_feature_list.feature_id in the IHM_FEATURE_LIST category. ; # _item.name "_ihm_derived_dihedral_restraint.feature_id_2" _item.category_id ihm_derived_dihedral_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_derived_dihedral_restraint.feature_id_2" _item_linked.parent_name "_ihm_feature_list.feature_id" # save_ # save__ihm_derived_dihedral_restraint.feature_id_3 _item_description.description ; The feature identifier for the third partner in the dihedral restraint. This data item is a pointer to _ihm_feature_list.feature_id in the IHM_FEATURE_LIST category. ; # _item.name "_ihm_derived_dihedral_restraint.feature_id_3" _item.category_id ihm_derived_dihedral_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_derived_dihedral_restraint.feature_id_3" _item_linked.parent_name "_ihm_feature_list.feature_id" # save_ # save__ihm_derived_dihedral_restraint.feature_id_4 _item_description.description ; The feature identifier for the fourth partner in the dihedral restraint. This data item is a pointer to _ihm_feature_list.feature_id in the IHM_FEATURE_LIST category. ; # _item.name "_ihm_derived_dihedral_restraint.feature_id_4" _item.category_id ihm_derived_dihedral_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_derived_dihedral_restraint.feature_id_4" _item_linked.parent_name "_ihm_feature_list.feature_id" # save_ # save__ihm_derived_dihedral_restraint.group_conditionality _item_description.description ; If a group of dihedrals are restrained together, this data item defines the conditionality based on which the restraint is applied in the modeling. ; # _item.name "_ihm_derived_dihedral_restraint.group_conditionality" _item.category_id ihm_derived_dihedral_restraint _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail ALL "All dihedrals in the group are required to be satisfied" ANY "Any one of the dihedrals in the group could be satisfied" # save_ # save__ihm_derived_dihedral_restraint.dihedral_lower_limit _item_description.description ; The lower limit to the threshold applied to this dihedral restraint in the integrative modeling task. ; # _item.name "_ihm_derived_dihedral_restraint.dihedral_lower_limit" _item.category_id ihm_derived_dihedral_restraint _item.mandatory_code no # _item_type.code float # _item_units.code degrees # save_ # save__ihm_derived_dihedral_restraint.dihedral_upper_limit _item_description.description ; The upper limit to the threshold applied to this dihedral restraint in the integrative modeling task. ; # _item.name "_ihm_derived_dihedral_restraint.dihedral_upper_limit" _item.category_id ihm_derived_dihedral_restraint _item.mandatory_code no # _item_type.code float # _item_units.code degrees # save_ # save__ihm_derived_dihedral_restraint.dihedral_lower_limit_esd _item_description.description " The estimated standard deviation of the lower limit dihedral threshold applied." # _item.name "_ihm_derived_dihedral_restraint.dihedral_lower_limit_esd" _item.category_id ihm_derived_dihedral_restraint _item.mandatory_code no # _item_type.code float # _item_units.code degrees # save_ # save__ihm_derived_dihedral_restraint.dihedral_upper_limit_esd _item_description.description " The estimated standard deviation of the upper limit dihedral threshold applied." # _item.name "_ihm_derived_dihedral_restraint.dihedral_upper_limit_esd" _item.category_id ihm_derived_dihedral_restraint _item.mandatory_code no # _item_type.code float # _item_units.code degrees # save_ # save__ihm_derived_dihedral_restraint.probability _item_description.description ; The real number that indicates the probability that the dihedral restraint is correct. This number should fall between 0.0 and 1.0. ; # _item.name "_ihm_derived_dihedral_restraint.probability" _item.category_id ihm_derived_dihedral_restraint _item.mandatory_code no # _item_type.code float # loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 1.0 1.0 1.0 # save_ # save__ihm_derived_dihedral_restraint.restraint_type _item_description.description " The type of dihedral restraint applied." # _item.name "_ihm_derived_dihedral_restraint.restraint_type" _item.category_id ihm_derived_dihedral_restraint _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value "lower bound" "upper bound" "lower and upper bound" harmonic # save_ # save__ihm_derived_dihedral_restraint.dihedral_threshold_mean _item_description.description " The dihedral threshold mean applied to the restraint." # _item.name "_ihm_derived_dihedral_restraint.dihedral_threshold_mean" _item.category_id ihm_derived_dihedral_restraint _item.mandatory_code no # _item_type.code float # _item_units.code degrees # save_ # save__ihm_derived_dihedral_restraint.dihedral_threshold_esd _item_description.description " The estimated standard deviation of the dihedral threshold applied to the restraint." # _item.name "_ihm_derived_dihedral_restraint.dihedral_threshold_esd" _item.category_id ihm_derived_dihedral_restraint _item.mandatory_code no # _item_type.code float # _item_units.code degrees # save_ # save__ihm_derived_dihedral_restraint.dataset_list_id _item_description.description ; Identifier to the input data from which the dihedral restraint is derived. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_derived_dihedral_restraint.dataset_list_id" _item.category_id ihm_derived_dihedral_restraint _item.mandatory_code no # _pdbx_item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_derived_dihedral_restraint.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save_ihm_geometric_object_list _category.description ; Data items in the IHM_GEOMETRIC_OBJECT_LIST category records the list of geometric objects used as restraints in the integrative modeling study. ; _category.id ihm_geometric_object_list _category.mandatory_code no # _category_key.name "_ihm_geometric_object_list.object_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_geometric_object_list.object_id _ihm_geometric_object_list.object_type _ihm_geometric_object_list.object_name _ihm_geometric_object_list.object_description 1 sphere . . 2 half-torus 'Nuclear membrane' 'Half-torus representing the nuclear membrane' # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_geometric_object_list # save_ # save__ihm_geometric_object_list.object_id _item_description.description " A unique identifier for the geometric object." # _item.name "_ihm_geometric_object_list.object_id" _item.category_id ihm_geometric_object_list _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_geometric_object_list.object_type _item_description.description " The type of geometric object." # _item.name "_ihm_geometric_object_list.object_type" _item.category_id ihm_geometric_object_list _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value sphere axis plane torus half-torus other # save_ # save__ihm_geometric_object_list.object_name _item_description.description " User-provided name for the object." # _item.name "_ihm_geometric_object_list.object_name" _item.category_id ihm_geometric_object_list _item.mandatory_code no # _item_type.code line # _item_examples.case "Nuclear membrane" # save_ # save__ihm_geometric_object_list.object_description _item_description.description " Brief description of the geometric object." # _item.name "_ihm_geometric_object_list.object_description" _item.category_id ihm_geometric_object_list _item.mandatory_code no # _item_type.code text # _item_examples.case "Half-torus representing the nuclear membrane" # save_ # save_ihm_geometric_object_center _category.description ; Data items in the IHM_GEOMETRIC_OBJECT_CENTER category records the center of geometric objects used as restraints in the integrative modeling study. ; _category.id ihm_geometric_object_center _category.mandatory_code no # _category_key.name "_ihm_geometric_object_center.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_geometric_object_center.id _ihm_geometric_object_center.xcoord _ihm_geometric_object_center.ycoord _ihm_geometric_object_center.zcoord 1 0.0 0.0 0.0 2 1.0 0.0 0.0 3 0.0 1.0 0.0 4 0.0 0.0 1.0 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_geometric_object_center # save_ # save__ihm_geometric_object_center.id _item_description.description " A unique identifier for the center." # _item.name "_ihm_geometric_object_center.id" _item.category_id ihm_geometric_object_center _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_geometric_object_center.xcoord _item_description.description " The x-coordinate of the center." # _item.name "_ihm_geometric_object_center.xcoord" _item.category_id ihm_geometric_object_center _item.mandatory_code yes # _item_type.code float # save_ # save__ihm_geometric_object_center.ycoord _item_description.description " The y-coordinate of the center." # _item.name "_ihm_geometric_object_center.ycoord" _item.category_id ihm_geometric_object_center _item.mandatory_code yes # _item_type.code float # save_ # save__ihm_geometric_object_center.zcoord _item_description.description " The z-coordinate of the center." # _item.name "_ihm_geometric_object_center.zcoord" _item.category_id ihm_geometric_object_center _item.mandatory_code yes # _item_type.code float # save_ # save_ihm_geometric_object_transformation _category.description ; Data items in the IHM_GEOMETRIC_OBJECT_TRANSFORMATION category records the details of the rotation matrix and translation vector applied for transforming the geometric object. If no transformation is provide, identity transformation is assumed. ; _category.id ihm_geometric_object_transformation _category.mandatory_code no # _category_key.name "_ihm_geometric_object_transformation.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; _ihm_geometric_object_transformation.id 1 _ihm_geometric_object_transformation.rot_matrix[1][1] 1.0 _ihm_geometric_object_transformation.rot_matrix[2][1] 0.0 _ihm_geometric_object_transformation.rot_matrix[3][1] 0.0 _ihm_geometric_object_transformation.rot_matrix[1][2] 0.0 _ihm_geometric_object_transformation.rot_matrix[2][2] 1.0 _ihm_geometric_object_transformation.rot_matrix[3][2] 0.0 _ihm_geometric_object_transformation.rot_matrix[1][3] 0.0 _ihm_geometric_object_transformation.rot_matrix[2][3] 0.0 _ihm_geometric_object_transformation.rot_matrix[3][3] 1.0 _ihm_geometric_object_transformation.tr_vector[1] 0.0 _ihm_geometric_object_transformation.tr_vector[2] 0.0 _ihm_geometric_object_transformation.tr_vector[3] 0.0 ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_geometric_object_transformation # save_ # save__ihm_geometric_object_transformation.id _item_description.description " A unique identifier for the transformation." # _item.name "_ihm_geometric_object_transformation.id" _item.category_id ihm_geometric_object_transformation _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_geometric_object_transformation.rot_matrix[1][1] _item_description.description " Data item [1][1] of the rotation matrix used in the transformation." # _item.name "_ihm_geometric_object_transformation.rot_matrix[1][1]" _item.category_id ihm_geometric_object_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_geometric_object_transformation.rot_matrix[2][1] _item_description.description " Data item [2][1] of the rotation matrix used in the transformation." # _item.name "_ihm_geometric_object_transformation.rot_matrix[2][1]" _item.category_id ihm_geometric_object_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_geometric_object_transformation.rot_matrix[3][1] _item_description.description " Data item [3][1] of the rotation matrix used in the transformation." # _item.name "_ihm_geometric_object_transformation.rot_matrix[3][1]" _item.category_id ihm_geometric_object_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_geometric_object_transformation.rot_matrix[1][2] _item_description.description " Data item [1][2] of the rotation matrix used in the transformation." # _item.name "_ihm_geometric_object_transformation.rot_matrix[1][2]" _item.category_id ihm_geometric_object_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_geometric_object_transformation.rot_matrix[2][2] _item_description.description " Data item [2][2] of the rotation matrix used in the transformation." # _item.name "_ihm_geometric_object_transformation.rot_matrix[2][2]" _item.category_id ihm_geometric_object_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_geometric_object_transformation.rot_matrix[3][2] _item_description.description " Data item [3][2] of the rotation matrix used in the transformation." # _item.name "_ihm_geometric_object_transformation.rot_matrix[3][2]" _item.category_id ihm_geometric_object_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_geometric_object_transformation.rot_matrix[1][3] _item_description.description " Data item [1][3] of the rotation matrix used in the transformation." # _item.name "_ihm_geometric_object_transformation.rot_matrix[1][3]" _item.category_id ihm_geometric_object_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_geometric_object_transformation.rot_matrix[2][3] _item_description.description " Data item [2][3] of the rotation matrix used in the transformation." # _item.name "_ihm_geometric_object_transformation.rot_matrix[2][3]" _item.category_id ihm_geometric_object_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_geometric_object_transformation.rot_matrix[3][3] _item_description.description " Data item [3][3] of the rotation matrix used in the transformation." # _item.name "_ihm_geometric_object_transformation.rot_matrix[3][3]" _item.category_id ihm_geometric_object_transformation _item.mandatory_code no # _item_sub_category.id matrix # _item_type.code float # save_ # save__ihm_geometric_object_transformation.tr_vector[1] _item_description.description " Data item [1] of the translation vector used in the transformation." # _item.name "_ihm_geometric_object_transformation.tr_vector[1]" _item.category_id ihm_geometric_object_transformation _item.mandatory_code no # _item_sub_category.id vector # _item_type.code float # save_ # save__ihm_geometric_object_transformation.tr_vector[2] _item_description.description " Data item [2] of the translation vector used in the transformation." # _item.name "_ihm_geometric_object_transformation.tr_vector[2]" _item.category_id ihm_geometric_object_transformation _item.mandatory_code no # _item_sub_category.id vector # _item_type.code float # save_ # save__ihm_geometric_object_transformation.tr_vector[3] _item_description.description " Data item [3] of the translation vector used in the transformation." # _item.name "_ihm_geometric_object_transformation.tr_vector[3]" _item.category_id ihm_geometric_object_transformation _item.mandatory_code no # _item_sub_category.id vector # _item_type.code float # save_ # save_ihm_geometric_object_sphere _category.description ; Data items in the IHM_GEOMETRIC_OBJECT_SPHERE category records the parameters of a sphere. ; _category.id ihm_geometric_object_sphere _category.mandatory_code no # _category_key.name "_ihm_geometric_object_sphere.object_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_geometric_object_sphere.object_id _ihm_geometric_object_sphere.center_id _ihm_geometric_object_sphere.transformation_id _ihm_geometric_object_sphere.radius_r 1 1 1 1.0 2 2 2 2.0 3 3 3 3.0 4 4 4 4.0 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_geometric_object_sphere # save_ # save__ihm_geometric_object_sphere.object_id _item_description.description ; Identifier to the geometric object. This data item is a pointer to the _ihm_geometric_object_list.object_id in the IHM_GEOMETRIC_OBJECT_LIST category. ; # _item.name "_ihm_geometric_object_sphere.object_id" _item.category_id ihm_geometric_object_sphere _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_geometric_object_sphere.object_id" _item_linked.parent_name "_ihm_geometric_object_list.object_id" # save_ # save__ihm_geometric_object_sphere.center_id _item_description.description ; Identifier to the description of the center. This data item is a pointer to the _ihm_geometric_object_center.id in the IHM_GEOMETRIC_OBJECT_CENTER category. ; # _item.name "_ihm_geometric_object_sphere.center_id" _item.category_id ihm_geometric_object_sphere _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_geometric_object_sphere.center_id" _item_linked.parent_name "_ihm_geometric_object_center.id" # save_ # save__ihm_geometric_object_sphere.transformation_id _item_description.description ; Identifier to the description of the transformation. This data item is a pointer to the _ihm_geometric_object_transformation.id in the IHM_GEOMETRIC_OBJECT_TRANSFORMATION category. If no transformation is provide, identity transformation is assumed. ; # _item.name "_ihm_geometric_object_sphere.transformation_id" _item.category_id ihm_geometric_object_sphere _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_geometric_object_sphere.transformation_id" _item_linked.parent_name "_ihm_geometric_object_transformation.id" # save_ # save__ihm_geometric_object_sphere.radius_r _item_description.description ' Radius "r" of the sphere.' # _item.name "_ihm_geometric_object_sphere.radius_r" _item.category_id ihm_geometric_object_sphere _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # save_ # save_ihm_geometric_object_torus _category.description ; Data items in the IHM_GEOMETRIC_OBJECT_TORUS category records the parameters of a torus. By definition, the base plane of the torus is the XY plane. The `ihm_geometric_object_transformation` category can be used to generate transformations to any other plane. ; _category.id ihm_geometric_object_torus _category.mandatory_code no # _category_key.name "_ihm_geometric_object_torus.object_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_geometric_object_torus.object_id _ihm_geometric_object_torus.center_id _ihm_geometric_object_torus.transformation_id _ihm_geometric_object_torus.major_radius_R _ihm_geometric_object_torus.minor_radius_r 1 1 1 5.0 1.0 2 2 2 5.0 2.0 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_geometric_object_torus # save_ # save__ihm_geometric_object_torus.object_id _item_description.description ; Identifier to the geometric object. This data item is a pointer to the _ihm_geometric_object_list.object_id in the IHM_GEOMETRIC_OBJECT_LIST category. ; # _item.name "_ihm_geometric_object_torus.object_id" _item.category_id ihm_geometric_object_torus _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_geometric_object_torus.object_id" _item_linked.parent_name "_ihm_geometric_object_list.object_id" # save_ # save__ihm_geometric_object_torus.center_id _item_description.description ; Identifier to the description of the center. This data item is a pointer to the _ihm_geometric_object_center.id in the IHM_GEOMETRIC_OBJECT_CENTER category. ; # _item.name "_ihm_geometric_object_torus.center_id" _item.category_id ihm_geometric_object_torus _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_geometric_object_torus.center_id" _item_linked.parent_name "_ihm_geometric_object_center.id" # save_ # save__ihm_geometric_object_torus.transformation_id _item_description.description ; Identifier to the description of the transformation. This data item is a pointer to the _ihm_geometric_object_transformation.id in the IHM_GEOMETRIC_OBJECT_TRANSFORMATION category. If no transformation is provide, identity transformation is assumed. ; # _item.name "_ihm_geometric_object_torus.transformation_id" _item.category_id ihm_geometric_object_torus _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_geometric_object_torus.transformation_id" _item_linked.parent_name "_ihm_geometric_object_transformation.id" # save_ # save__ihm_geometric_object_torus.major_radius_R _item_description.description ' Major radius "R" of the torus.' # _item.name "_ihm_geometric_object_torus.major_radius_R" _item.category_id ihm_geometric_object_torus _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_geometric_object_torus.minor_radius_r _item_description.description ' Minor radius "r" of the torus.' # _item.name "_ihm_geometric_object_torus.minor_radius_r" _item.category_id ihm_geometric_object_torus _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # save_ # save_ihm_geometric_object_half_torus _category.description ; Data items in the IHM_GEOMETRIC_OBJECT_HALF_TORUS category records the parameters of half-torus that represents a membrane. ; _category.id ihm_geometric_object_half_torus _category.mandatory_code no # _category_key.name "_ihm_geometric_object_half_torus.object_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_geometric_object_half_torus.object_id _ihm_geometric_object_half_torus.thickness_th _ihm_geometric_object_half_torus.section 1 1.0 inner 2 2.0 inner # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_geometric_object_half_torus # save_ # save__ihm_geometric_object_half_torus.object_id _item_description.description ; Identifier to the geometric object. This data item is a pointer to the _ihm_geometric_object_torus.object_id in the IHM_GEOMETRIC_OBJECT_TORUS category. ; # _item.name "_ihm_geometric_object_half_torus.object_id" _item.category_id ihm_geometric_object_half_torus _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_geometric_object_half_torus.object_id" _item_linked.parent_name "_ihm_geometric_object_torus.object_id" # save_ # save__ihm_geometric_object_half_torus.thickness_th _item_description.description ' Thickness "th" of the half-torus.' # _item.name "_ihm_geometric_object_half_torus.thickness_th" _item.category_id ihm_geometric_object_half_torus _item.mandatory_code yes # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_geometric_object_half_torus.section _item_description.description " The section of the torus representing the half-torus." # _item.name "_ihm_geometric_object_half_torus.section" _item.category_id ihm_geometric_object_half_torus _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value "inner half" "outer half" other # save_ # save_ihm_geometric_object_axis _category.description ; Data items in the IHM_GEOMETRIC_OBJECT_AXIS category records the details of an axis used in a spatial restraint. ; _category.id ihm_geometric_object_axis _category.mandatory_code no # _category_key.name "_ihm_geometric_object_axis.object_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_geometric_object_axis.object_id _ihm_geometric_object_axis.axis_type 1 x-axis 2 y-axis 3 z-axis # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_geometric_object_axis # save_ # save__ihm_geometric_object_axis.object_id _item_description.description ; Identifier to the geometric object. This data item is a pointer to the _ihm_geometric_object_list.object_id in the IHM_GEOMETRIC_OBJECT_LIST category. ; # _item.name "_ihm_geometric_object_axis.object_id" _item.category_id ihm_geometric_object_axis _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_geometric_object_axis.object_id" _item_linked.parent_name "_ihm_geometric_object_list.object_id" # save_ # save__ihm_geometric_object_axis.axis_type _item_description.description " The type of axis." # _item.name "_ihm_geometric_object_axis.axis_type" _item.category_id ihm_geometric_object_axis _item.mandatory_code yes # _item_type.code code # loop_ _item_enumeration.value x-axis y-axis z-axis # save_ # save__ihm_geometric_object_axis.transformation_id _item_description.description ; Identifier to the description of the transformation. This data item is a pointer to the _ihm_geometric_object_transformation.id in the IHM_GEOMETRIC_OBJECT_TRANSFORMATION category. If no transformation is provide, identity transformation is assumed. ; # _item.name "_ihm_geometric_object_axis.transformation_id" _item.category_id ihm_geometric_object_axis _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_geometric_object_axis.transformation_id" _item_linked.parent_name "_ihm_geometric_object_transformation.id" # save_ # save_ihm_geometric_object_plane _category.description ; Data items in the IHM_GEOMETRIC_OBJECT_PLANE category records the details of a plane used in a spatial restraint. ; _category.id ihm_geometric_object_plane _category.mandatory_code no # _category_key.name "_ihm_geometric_object_plane.object_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_geometric_object_plane.object_id _ihm_geometric_object_plane.plane_type 1 xy-plane 2 yz-plane 3 xz-plane # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_geometric_object_plane # save_ # save__ihm_geometric_object_plane.object_id _item_description.description ; Identifier to the geometric object. This data item is a pointer to the _ihm_geometric_object_list.object_id in the IHM_GEOMETRIC_OBJECT_LIST category. ; # _item.name "_ihm_geometric_object_plane.object_id" _item.category_id ihm_geometric_object_plane _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_geometric_object_plane.object_id" _item_linked.parent_name "_ihm_geometric_object_list.object_id" # save_ # save__ihm_geometric_object_plane.plane_type _item_description.description " The type of plane." # _item.name "_ihm_geometric_object_plane.plane_type" _item.category_id ihm_geometric_object_plane _item.mandatory_code yes # _item_type.code code # loop_ _item_enumeration.value xy-plane yz-plane xz-plane # save_ # save__ihm_geometric_object_plane.transformation_id _item_description.description ; Identifier to the description of the transformation. This data item is a pointer to the _ihm_geometric_object_transformation.id in the IHM_GEOMETRIC_OBJECT_TRANSFORMATION category. If no transformation is provide, identity transformation is assumed. ; # _item.name "_ihm_geometric_object_plane.transformation_id" _item.category_id ihm_geometric_object_plane _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_geometric_object_plane.transformation_id" _item_linked.parent_name "_ihm_geometric_object_transformation.id" # save_ # save_ihm_geometric_object_distance_restraint _category.description ; Data items in the IHM_GEOMETRIC_OBJECT_DISTANCE_RESTRAINT category records the details of distance restraints involving geometric objects. If the geometric object involved is a plane, then the distance is along the normal following the right-hand rule. So for the xy plane, distance is along the z axis in the positive direction, 'above' the plane such that negative distances corresponded to positions below the plane. ; _category.id ihm_geometric_object_distance_restraint _category.mandatory_code no # _category_key.name "_ihm_geometric_object_distance_restraint.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_geometric_object_distance_restraint.id _ihm_geometric_object_distance_restraint.object_id _ihm_geometric_object_distance_restraint.feature_id _ihm_geometric_object_distance_restraint.object_characteristic _ihm_geometric_object_distance_restraint.restraint_type _ihm_geometric_object_distance_restraint.harmonic_force_constant _ihm_geometric_object_distance_restraint.dataset_list_id 1 1 21 'inner surface' 'harmonic' 1.0 1 2 1 22 'inner surface' 'harmonic' 1.0 1 3 1 23 'inner surface' 'harmonic' 1.0 1 4 1 24 'inner surface' 'harmonic' 1.0 1 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_geometric_object_distance_restraint # save_ # save__ihm_geometric_object_distance_restraint.id _item_description.description " A unique id for the geometric object distance restraint." # _item.name "_ihm_geometric_object_distance_restraint.id" _item.category_id ihm_geometric_object_distance_restraint _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_geometric_object_distance_restraint.object_id _item_description.description ; Identifier to the geometric object involved in the distance restraint. This data item is a pointer to the _ihm_geometric_object_list.object_id in the IHM_GEOMETRIC_OBJECT_LIST category. ; # _item.name "_ihm_geometric_object_distance_restraint.object_id" _item.category_id ihm_geometric_object_distance_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_geometric_object_distance_restraint.object_id" _item_linked.parent_name "_ihm_geometric_object_list.object_id" # save_ # save__ihm_geometric_object_distance_restraint.feature_id _item_description.description ; Identifier to the molecular feature involved in the distance restraint. This data item is a pointer to the _ihm_feature_list.feature_id in the IHM_FEATURE_LIST category. ; # _item.name "_ihm_geometric_object_distance_restraint.feature_id" _item.category_id ihm_geometric_object_distance_restraint _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_geometric_object_distance_restraint.feature_id" _item_linked.parent_name "_ihm_feature_list.feature_id" # save_ # save__ihm_geometric_object_distance_restraint.object_characteristic _item_description.description " The characteristic of the geometric object used in the restraint." # _item.name "_ihm_geometric_object_distance_restraint.object_characteristic" _item.category_id ihm_geometric_object_distance_restraint _item.mandatory_code no # _item_type.code line # loop_ _item_enumeration.value center "inner surface" "outer surface" axis plane other # save_ # save__ihm_geometric_object_distance_restraint.restraint_type _item_description.description " The type of restraint applied." # _item.name "_ihm_geometric_object_distance_restraint.restraint_type" _item.category_id ihm_geometric_object_distance_restraint _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value "upper bound" "lower bound" "lower and upper bound" harmonic other # save_ # save__ihm_geometric_object_distance_restraint.harmonic_force_constant _item_description.description " The harmonic force constant, if applicable." # _item.name "_ihm_geometric_object_distance_restraint.harmonic_force_constant" _item.category_id ihm_geometric_object_distance_restraint _item.mandatory_code no # _item_type.code float # save_ # save__ihm_geometric_object_distance_restraint.group_conditionality _item_description.description ; If a group of atoms or residues are restrained, this data item defines the conditionality based on which the restraint is applied in the modeling. ; # _item.name "_ihm_geometric_object_distance_restraint.group_conditionality" _item.category_id ihm_geometric_object_distance_restraint _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail ALL "All distances among the group of atoms or residues are restrained" ANY "Any one of the distances among the group of atoms or residues could be satisfied" # save_ # save__ihm_geometric_object_distance_restraint.distance_lower_limit _item_description.description " The lower limit to the distance threshold, if applicable." # _item.name "_ihm_geometric_object_distance_restraint.distance_lower_limit" _item.category_id ihm_geometric_object_distance_restraint _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_geometric_object_distance_restraint.distance_upper_limit _item_description.description " The upper limit to the distance threshold, if applicable." # _item.name "_ihm_geometric_object_distance_restraint.distance_upper_limit" _item.category_id ihm_geometric_object_distance_restraint _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_geometric_object_distance_restraint.distance_lower_limit_esd _item_description.description " The estimated standard deviation of the lower limit distance threshold, if applicable." # _item.name "_ihm_geometric_object_distance_restraint.distance_lower_limit_esd" _item.category_id ihm_geometric_object_distance_restraint _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_geometric_object_distance_restraint.distance_upper_limit_esd _item_description.description " The estimated standard deviation of the upper limit distance threshold, if applicable." # _item.name "_ihm_geometric_object_distance_restraint.distance_upper_limit_esd" _item.category_id ihm_geometric_object_distance_restraint _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # save_ # save__ihm_geometric_object_distance_restraint.distance_probability _item_description.description ; The real number that indicates the probability that the distance restraint is correct. This number should fall between 0.0 and 1.0. ; # _item.name "_ihm_geometric_object_distance_restraint.distance_probability" _item.category_id ihm_geometric_object_distance_restraint _item.mandatory_code no # _item_type.code float # loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 1.0 1.0 1.0 # save_ # save__ihm_geometric_object_distance_restraint.dataset_list_id _item_description.description ; Identifier to the input data from which the restraint is derived. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category. ; # _item.name "_ihm_geometric_object_distance_restraint.dataset_list_id" _item.category_id ihm_geometric_object_distance_restraint _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_geometric_object_distance_restraint.dataset_list_id" _item_linked.parent_name "_ihm_dataset_list.id" # save_ # save__ihm_geometric_object_distance_restraint.details _item_description.description ; Additional details about the geometric object distance restraints, especially if _ihm_geometric_object_distance_restraint.restraint_type or _ihm_geometric_object_distance_restraint.object_characteristic is "other". ; # _item.name "_ihm_geometric_object_distance_restraint.details" _item.category_id ihm_geometric_object_distance_restraint _item.mandatory_code no # _item_type.code text # save_ # save_ihm_entry_collection _category.description ; Data items in the IHM_ENTRY_COLLECTION category identify a collection of IHM entries belonging to a single deposition or group. ; _category.id ihm_entry_collection _category.mandatory_code no # _category_key.name "_ihm_entry_collection.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_entry_collection.id _ihm_entry_collection.name _ihm_entry_collection.details 1 . . # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_entry_collection # save_ # save__ihm_entry_collection.id _item_description.description " A unique identifier for the entry collection assigned by the archive." # _item.name "_ihm_entry_collection.id" _item.category_id ihm_entry_collection _item.mandatory_code yes # _item_type.code code # save_ # save__ihm_entry_collection.name _item_description.description " Name for the entry collection." # _item.name "_ihm_entry_collection.name" _item.category_id ihm_entry_collection _item.mandatory_code no # _item_type.code line # save_ # save__ihm_entry_collection.details _item_description.description " Details about the entry collection." # _item.name "_ihm_entry_collection.details" _item.category_id ihm_entry_collection _item.mandatory_code no # _item_type.code text # save_ # save_ihm_entry_collection_mapping _category.description ; Data items in the IHM_ENTRY_COLLECTION_MAPPING category identify the entries that belong to a collection. ; _category.id ihm_entry_collection_mapping _category.mandatory_code no # loop_ _category_key.name "_ihm_entry_collection_mapping.collection_id" "_ihm_entry_collection_mapping.entry_id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; loop_ _ihm_entry_collection_mapping.collection_id _ihm_entry_collection_mapping.entry_id PDBDEV_G_1000001 PDBDEV_00000165 PDBDEV_G_1000001 PDBDEV_00000198 # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_entry_collection_mapping # save_ # save__ihm_entry_collection_mapping.collection_id _item_description.description ; Identifier for the entry collection. This data item is a pointer to _ihm_entry_collection.id in the IHM_ENTRY_COLLECTION category. ; # _item.name "_ihm_entry_collection_mapping.collection_id" _item.category_id ihm_entry_collection_mapping _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_entry_collection_mapping.collection_id" _item_linked.parent_name "_ihm_entry_collection.id" # save_ # save__ihm_entry_collection_mapping.entry_id _item_description.description ; Identifier for the entry. This data item is a pointer to _entry.id in the ENTRY category. ; # _item.name "_ihm_entry_collection_mapping.entry_id" _item.category_id ihm_entry_collection_mapping _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_ihm_entry_collection_mapping.entry_id" _item_linked.parent_name "_entry.id" # save_ # save_ihm_multi_state_scheme _category.description ; Data items in the IHM_MULTI_STATE_SCHEME category provide details about collection of multiple states that can form a connected/ordered scheme. ; _category.id ihm_multi_state_scheme _category.mandatory_code no # _category_key.name "_ihm_multi_state_scheme.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_multi_state_scheme # save_ # save__ihm_multi_state_scheme.id _item_description.description " A unique identifier for the category." # _item.name "_ihm_multi_state_scheme.id" _item.category_id ihm_multi_state_scheme _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_multi_state_scheme.name _item_description.description " Name for the multi-state scheme." # _item.name "_ihm_multi_state_scheme.name" _item.category_id ihm_multi_state_scheme _item.mandatory_code no # _item_type.code line # save_ # save__ihm_multi_state_scheme.details _item_description.description " Details about the multi-state scheme." # _item.name "_ihm_multi_state_scheme.details" _item.category_id ihm_multi_state_scheme _item.mandatory_code no # _item_type.code text # save_ # save_ihm_multi_state_scheme_connectivity _category.description ; Data items in the IHM_MULTI_STATE_SCHEME_CONNECTIVITY category record the details of the ordered connectivities among states in a multi-state scheme. ; _category.id ihm_multi_state_scheme_connectivity _category.mandatory_code no # _category_key.name "_ihm_multi_state_scheme_connectivity.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_multi_state_scheme_connectivity # save_ # save__ihm_multi_state_scheme_connectivity.id _item_description.description " A unique identifier for the category." # _item.name "_ihm_multi_state_scheme_connectivity.id" _item.category_id ihm_multi_state_scheme_connectivity _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_multi_state_scheme_connectivity.scheme_id _item_description.description ; An identifier for the multi-state scheme. This data item is a pointer to _ihm_multi_state_scheme.id in the IHM_MULTI_STATE_SCHEME data category. ; # _item.name "_ihm_multi_state_scheme_connectivity.scheme_id" _item.category_id ihm_multi_state_scheme_connectivity _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_multi_state_scheme_connectivity.scheme_id" _item_linked.parent_name "_ihm_multi_state_scheme.id" # save_ # save__ihm_multi_state_scheme_connectivity.begin_state_id _item_description.description ; An identifier for the starting state in the multi-state scheme. This data item is a pointer to _ihm_multi_state_modeling.state_id in the IHM_MULTI_STATE_MODELING data category. ; # _item.name "_ihm_multi_state_scheme_connectivity.begin_state_id" _item.category_id ihm_multi_state_scheme_connectivity _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_multi_state_scheme_connectivity.begin_state_id" _item_linked.parent_name "_ihm_multi_state_modeling.state_id" # save_ # save__ihm_multi_state_scheme_connectivity.end_state_id _item_description.description ; An identifier for the ending state in the multi-state scheme. This data item is a pointer to _ihm_multi_state_modeling.state_id in the IHM_MULTI_STATE_MODELING data category. ; # _item.name "_ihm_multi_state_scheme_connectivity.end_state_id" _item.category_id ihm_multi_state_scheme_connectivity _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_multi_state_scheme_connectivity.end_state_id" _item_linked.parent_name "_ihm_multi_state_modeling.state_id" # save_ # save__ihm_multi_state_scheme_connectivity.dataset_group_id _item_description.description ; Identifier for the dataset group from which the multi state scheme is obtained. This data item is a pointer to _ihm_dataset_group.id in the IHM_DATASET_GROUP data category. ; # _item.name "_ihm_multi_state_scheme_connectivity.dataset_group_id" _item.category_id ihm_multi_state_scheme_connectivity _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_multi_state_scheme_connectivity.dataset_group_id" _item_linked.parent_name "_ihm_dataset_group.id" # save_ # save__ihm_multi_state_scheme_connectivity.details _item_description.description " Details about the multi-state scheme connectivity." # _item.name "_ihm_multi_state_scheme_connectivity.details" _item.category_id ihm_multi_state_scheme_connectivity _item.mandatory_code no # _item_type.code text # save_ # save_ihm_kinetic_rate _category.description ; Data items in the IHM_KINETIC_RATE category records the details of kinetic rates obtained from biophysical experiments. ; _category.id ihm_kinetic_rate _category.mandatory_code no # _category_key.name "_ihm_kinetic_rate.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; #...abbreviated... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_kinetic_rate # save_ # save__ihm_kinetic_rate.id _item_description.description " An identifier for the kinetic rate." # _item.name "_ihm_kinetic_rate.id" _item.category_id ihm_kinetic_rate _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_kinetic_rate.transition_rate_constant _item_description.description " The transition rate constant per second." # _item.name "_ihm_kinetic_rate.transition_rate_constant" _item.category_id ihm_kinetic_rate _item.mandatory_code no # _item_type.code float # _item_units.code reciprocal_seconds # save_ # save__ihm_kinetic_rate.equilibrium_constant _item_description.description " The equilibrium constant." # _item.name "_ihm_kinetic_rate.equilibrium_constant" _item.category_id ihm_kinetic_rate _item.mandatory_code no # _item_type.code float # save_ # save__ihm_kinetic_rate.equilibrium_constant_determination_method _item_description.description " Method used to determine the equilibrium constant." # _item.name "_ihm_kinetic_rate.equilibrium_constant_determination_method" _item.category_id ihm_kinetic_rate _item.mandatory_code no # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail "from population" "equilibrium constant is determined from population" "from kinetic rates" "equilibrium constant is determined from kinetic rates, kAB/kBA" other "equilibrium constant is determined from another method not listed" # save_ # save__ihm_kinetic_rate.equilibrium_constant_unit _item_description.description ; Unit of the equilibrium constant, if applicable. If the kinetics describes a conformational change, then the equilibrium constant will not have a unit. If however a complex is involved, then a unit may be necessary. ; # _item.name "_ihm_kinetic_rate.equilibrium_constant_unit" _item.category_id ihm_kinetic_rate _item.mandatory_code no # _item_type.code line # save_ # save__ihm_kinetic_rate.details _item_description.description " Additional details about the kinetic rate." # _item.name "_ihm_kinetic_rate.details" _item.category_id ihm_kinetic_rate _item.mandatory_code no # _item_type.code text # save_ # save__ihm_kinetic_rate.scheme_connectivity_id _item_description.description ; Identifier for the multi-state scheme connectivity. This data item is a pointer to _ihm_multi_state_scheme_connectivity.id in the IHM_MULTI_STATE_SCHEME_CONNECTIVITY category. ; # _item.name "_ihm_kinetic_rate.scheme_connectivity_id" _item.category_id ihm_kinetic_rate _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_kinetic_rate.scheme_connectivity_id" _item_linked.parent_name "_ihm_multi_state_scheme_connectivity.id" # save_ # save__ihm_kinetic_rate.dataset_group_id _item_description.description ; Identifier for the dataset group from which the kinetic rates are obtained. This data item is a pointer to _ihm_dataset_group.id in the IHM_DATASET_GROUP data category. ; # _item.name "_ihm_kinetic_rate.dataset_group_id" _item.category_id ihm_kinetic_rate _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_kinetic_rate.dataset_group_id" _item_linked.parent_name "_ihm_dataset_group.id" # save_ # save__ihm_kinetic_rate.external_file_id _item_description.description ; Identifier for the external file corresponding to the kinetic rate measurement. This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES data category. ; # _item.name "_ihm_kinetic_rate.external_file_id" _item.category_id ihm_kinetic_rate _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_kinetic_rate.external_file_id" _item_linked.parent_name "_ihm_external_files.id" # save_ # save_ihm_relaxation_time _category.description ; Data items in the IHM_RELAXATION_TIME category records the details of the relaxation times obtained from biophysical experiments. ; _category.id ihm_relaxation_time _category.mandatory_code no # _category_key.name "_ihm_relaxation_time.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_relaxation_time # save_ # save__ihm_relaxation_time.id _item_description.description " A unique identifier for the relaxation time." # _item.name "_ihm_relaxation_time.id" _item.category_id ihm_relaxation_time _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_relaxation_time.value _item_description.description " Relaxation time value." # _item.name "_ihm_relaxation_time.value" _item.category_id ihm_relaxation_time _item.mandatory_code yes # _item_type.code float # save_ # save__ihm_relaxation_time.unit _item_description.description " Relaxation time unit." # _item.name "_ihm_relaxation_time.unit" _item.category_id ihm_relaxation_time _item.mandatory_code yes # _item_type.code code # loop_ _item_enumeration.value seconds milliseconds microseconds # save_ # save__ihm_relaxation_time.amplitude _item_description.description " Relaxation time amplitude." # _item.name "_ihm_relaxation_time.amplitude" _item.category_id ihm_relaxation_time _item.mandatory_code no # _item_type.code float # save_ # save__ihm_relaxation_time.dataset_group_id _item_description.description ; Identifier for the dataset group from which the relaxation time is obtained. This data item is a pointer to _ihm_dataset_group.id in the IHM_DATASET_GROUP data category. ; # _item.name "_ihm_relaxation_time.dataset_group_id" _item.category_id ihm_relaxation_time _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_relaxation_time.dataset_group_id" _item_linked.parent_name "_ihm_dataset_group.id" # save_ # save__ihm_relaxation_time.external_file_id _item_description.description ; Identifier for the external file corresponding to the relaxation time measurement. This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES data category. ; # _item.name "_ihm_relaxation_time.external_file_id" _item.category_id ihm_relaxation_time _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_relaxation_time.external_file_id" _item_linked.parent_name "_ihm_external_files.id" # save_ # save__ihm_relaxation_time.details _item_description.description " Additional details regarding the relaxation time." # _item.name "_ihm_relaxation_time.details" _item.category_id ihm_relaxation_time _item.mandatory_code no # _item_type.code text # save_ # save_ihm_relaxation_time_multi_state_scheme _category.description ; Data items in the IHM_RELAXATION_TIME_MULTI_STATE_SCHEME category map the experimentally measured relaxation times with the multi-state schemes. ; _category.id ihm_relaxation_time_multi_state_scheme _category.mandatory_code no # _category_key.name "_ihm_relaxation_time_multi_state_scheme.id" # loop_ _category_group.id inclusive_group ihm_group # _category_examples.detail ; Example 1 - ; _category_examples.case ; # ... abbreviated ... ; # _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ihm_relaxation_time_multi_state_scheme # save_ # save__ihm_relaxation_time_multi_state_scheme.id _item_description.description " A unique identifier for the category." # _item.name "_ihm_relaxation_time_multi_state_scheme.id" _item.category_id ihm_relaxation_time_multi_state_scheme _item.mandatory_code yes # _item_type.code int # save_ # save__ihm_relaxation_time_multi_state_scheme.relaxation_time_id _item_description.description ; Identifier for the relaxation_time. This data item is a pointer to _ihm_relaxation_time.id in the IHM_RELAXATION_TIME data category. ; # _item.name "_ihm_relaxation_time_multi_state_scheme.relaxation_time_id" _item.category_id ihm_relaxation_time_multi_state_scheme _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_relaxation_time_multi_state_scheme.relaxation_time_id" _item_linked.parent_name "_ihm_relaxation_time.id" # save_ # save__ihm_relaxation_time_multi_state_scheme.scheme_id _item_description.description ; Identifier for the multi-state scheme. This data item is a pointer to _ihm_multi_state_scheme.id in the IHM_MULTI_STATE_SCHEME data category. ; # _item.name "_ihm_relaxation_time_multi_state_scheme.scheme_id" _item.category_id ihm_relaxation_time_multi_state_scheme _item.mandatory_code yes # _item_type.code int # _item_linked.child_name "_ihm_relaxation_time_multi_state_scheme.scheme_id" _item_linked.parent_name "_ihm_multi_state_scheme.id" # save_ # save__ihm_relaxation_time_multi_state_scheme.scheme_connectivity_id _item_description.description ; Identifier for the multi-state scheme connectivity. This data item is a pointer to _ihm_multi_state_scheme_connectivity.id in the IHM_MULTI_STATE_SCHEME_CONNECTIVITY data category. ; # _item.name "_ihm_relaxation_time_multi_state_scheme.scheme_connectivity_id" _item.category_id ihm_relaxation_time_multi_state_scheme _item.mandatory_code no # _item_type.code int # _item_linked.child_name "_ihm_relaxation_time_multi_state_scheme.scheme_connectivity_id" _item_linked.parent_name "_ihm_multi_state_scheme_connectivity.id" # save_ # save__ihm_relaxation_time_multi_state_scheme.details _item_description.description " Additional details about the relaxation time measurement." # _item.name "_ihm_relaxation_time_multi_state_scheme.details" _item.category_id ihm_relaxation_time_multi_state_scheme _item.mandatory_code no # _item_type.code text # save_ #