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# -------------------------------------------------------------------------------------------------------------------------
#
# File: ihm-extension.dic
# Date: 03-JAN-2019
#
# Dictionary extension for integrative/hybrid models.
#
# -------------------------------------------------------------------------------------------------------------------------
data_ihm-extension.dic
_datablock.id ihm-extension.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/IHM-dictionary.
I/H structural models that are compliant to this extension dictionary can be deposited
to the PDB-Dev prototype deposition and archiving system (https://pdb-dev.wwpdb.org).
;
_dictionary.title ihm-extension.dic
_dictionary.datablock_id ihm-extension.dic
_dictionary.version 0.139
#
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 2018-10-4
;
Changes (bv):
+ Added DSSO crosslinker
+ Updated parent-child relationships for several data items:
_ihm_starting_model_details.entity_id, _ihm_model_representation.entity_id,
_ihm_struct_assembly.entity_id, _ihm_localization_density_files.entity_id,
_ihm_starting_model_coord.entity_id, _ihm_starting_model_coord.comp_id,
_ihm_sphere_obj_site.entity_id, _ihm_gaussian_obj_site.entity_id,
_ihm_gaussian_obj_ensemble.entity_id
+ Updated _item_type.code for _ihm_external_files.file_path
;
0.136 2018-10-5
;
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
;
#########################
## CATEGORY_GROUP_LIST ##
#########################
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.
;
'ihm_group'
'inclusive_group'
; Categories that describe the integrative/hybrid (I/H) methods extension dictionary.
;
####################
## ITEM_TYPE_LIST ##
####################
#
#
# The regular expressions defined here are not compliant
# with the POSIX 1003.2 standard as they include the
# '\n' and '\t' special characters. These regular expressions
# have been tested using version 0.12 of Richard Stallman's
# GNU regular expression library in POSIX mode.
#
#
##############################################################################
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...
;
#####################
## ITEM_UNITS_LIST ##
#####################
loop_
_item_units_list.code
_item_units_list.detail
'angstroms' 'Angstroms (metres * 10^(-10)^)'
'angstroms_squared' 'Angstroms squared (metres * 10^(-10)^)^2^'
'8pi2_angstroms_squared' '8pi^2^ * Angstroms squared (metres * 10^(-10)^)^2^'
'reciprocal_seconds' 'reciprocal seconds (seconds^(-1)^)'
################################
## IHM_STARTING_MODEL_DETAILS ##
################################
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
loop_
_category_key.name '_ihm_starting_model_details.starting_model_id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
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.seq_id_begin
_ihm_starting_model_details.seq_id_end
_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 7 726 'comparative model' A 0 5
Nup85-m1 2 Nup85 B 67 743 'comparative model' B 0 9
Nup120-m1 3 Nup120 C 1 1037 'comparative model' C 0 13
Nup133-m1 4 Nup133 D 56 480 'comparative model' D 0 15
Nup133-m2 4 Nup133 D 490 1155 'comparative model' D 0 16
Nup145c-m1 5 Nup145c E 126 553 'comparative model' E 0 19
Seh1-m1 6 Seh1 F 1 346 'experimental model' A 0 20
Sec13-m1 7 Sec13 G 2 296 '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
_item_linked.child_name '_ihm_starting_model_details.entity_description'
_item_linked.parent_name '_entity.pdbx_description'
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.seq_id_begin
_item_description.description
; The leading residue index for the sequence segment modeled using this starting model.
This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
;
_item.name '_ihm_starting_model_details.seq_id_begin'
_item.category_id ihm_starting_model_details
_item.mandatory_code no
_item_type.code int
_item_linked.child_name '_ihm_starting_model_details.seq_id_begin'
_item_linked.parent_name '_entity_poly_seq.num'
save_
save__ihm_starting_model_details.seq_id_end
_item_description.description
; The trailing residue index for the sequence segment modeled using this starting model.
This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
;
_item.name '_ihm_starting_model_details.seq_id_end'
_item.category_id ihm_starting_model_details
_item.mandatory_code no
_item_type.code int
_item_linked.child_name '_ihm_starting_model_details.seq_id_end'
_item_linked.parent_name '_entity_poly_seq.num'
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_
#####################################
## IHM_STARTING_COMPARATIVE_MODELS ##
#####################################
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
loop_
_category_key.name '_ihm_starting_comparative_models.ordinal_id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_ihm_starting_comparative_models.ordinal_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.ordinal_id
_item_description.description
; A unique identifier for the starting comparative model.
;
_item.name '_ihm_starting_comparative_models.ordinal_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_denominator'
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_
#######################################
## IHM_STARTING_COMPUTATIONAL_MODELS ##
#######################################
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
loop_
_category_key.name '_ihm_starting_computational_models.starting_model_id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
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 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 yes
_item_type.code int
_item_linked.child_name '_ihm_starting_computational_models.software_id'
_item_linked.parent_name '_software.pdbx_ordinal'
save_
################################
## IHM_STARTING_MODEL_SEQ_DIF ##
################################
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.ordinal_id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
loop_
_ihm_starting_model_seq_dif.ordinal_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.ordinal_id
_item_description.description
; A unique identifier for the entry.
;
_item.name '_ihm_starting_model_seq_dif.ordinal_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_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_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_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_
##############################
## IHM_MODEL_REPRESENTATION ##
##############################
save_ihm_model_representation
_category.description
; Data items in the IHM_MODEL_REPRESENTATION category records the
details about the architecture and representation of structural
models created by the integrative model building tasks. This
category handles the multi-scale model representation, if employed.
;
_category.id ihm_model_representation
_category.mandatory_code no
loop_
_category_key.name '_ihm_model_representation.ordinal_id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_ihm_model_representation.ordinal_id
_ihm_model_representation.representation_id
_ihm_model_representation.segment_id
_ihm_model_representation.entity_id
_ihm_model_representation.entity_description
_ihm_model_representation.entity_asym_id
_ihm_model_representation.seq_id_begin
_ihm_model_representation.seq_id_end
_ihm_model_representation.model_object_primitive
_ihm_model_representation.starting_model_id
_ihm_model_representation.model_mode
_ihm_model_representation.model_granularity
_ihm_model_representation.model_object_count
1 1 1 1 Nup84 A 1 6 sphere Nup84-m1 flexible by-feature 1
2 1 2 1 Nup84 A 7 20 sphere Nup84-m1 rigid by-residue .
3 1 3 1 Nup84 A 21 26 sphere Nup84-m1 flexible by-feature 1
4 1 4 1 Nup84 A 27 80 sphere Nup84-m1 rigid by-residue .
5 1 5 1 Nup84 A 81 95 sphere Nup84-m1 flexible by-feature 1
6 1 6 1 Nup84 A 96 126 sphere Nup84-m1 rigid by-residue .
7 1 6 1 Nup84 A 96 126 sphere Nup84-m1 flexible by-feature 3
8 1 7 1 Nup84 A 127 135 sphere Nup84-m1 flexible by-feature 1
# ... abbreviated ...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_pdbx_category_context.type CONTRIBUTED
_pdbx_category_context.category_id ihm_model_representation
save_
save__ihm_model_representation.ordinal_id
_item_description.description
; A unique identifier for the model details record.
;
_item.name '_ihm_model_representation.ordinal_id'
_item.category_id ihm_model_representation
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_model_representation.representation_id
_item_description.description
; An identifier that collects or groups together a set of representations.
This data item may be used to identify a complete model representation.
;
_item.name '_ihm_model_representation.representation_id'
_item.category_id ihm_model_representation
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_model_representation.segment_id
_item_description.description
; An identifier for the residue range segment within the structural model.
;
_item.name '_ihm_model_representation.segment_id'
_item.category_id ihm_model_representation
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_model_representation.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.entity_id'
_item.category_id ihm_model_representation
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ihm_model_representation.entity_id'
_item_linked.parent_name '_entity.id'
save_
save__ihm_model_representation.entity_description
_item_description.description
; A text description of the molecular entity
;
_item.name '_ihm_model_representation.entity_description'
_item.category_id ihm_model_representation
_item.mandatory_code no
_item_type.code line
_item_linked.child_name '_ihm_model_representation.entity_description'
_item_linked.parent_name '_entity.pdbx_description'
save_
save__ihm_model_representation.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.entity_asym_id'
_item.category_id ihm_model_representation
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ihm_model_representation.entity_asym_id'
_item_linked.parent_name '_struct_asym.id'
save_
save__ihm_model_representation.seq_id_begin
_item_description.description
; The leading residue index for the sequence segment modeled using this starting model.
This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
;
_item.name '_ihm_model_representation.seq_id_begin'
_item.category_id ihm_model_representation
_item.mandatory_code no
_item_type.code int
_item_linked.child_name '_ihm_model_representation.seq_id_begin'
_item_linked.parent_name '_entity_poly_seq.num'
save_
save__ihm_model_representation.seq_id_end
_item_description.description
; The trailing residue index for the sequence segment modeled using this starting model.
This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
;
_item.name '_ihm_model_representation.seq_id_end'
_item.category_id ihm_model_representation
_item.mandatory_code no
_item_type.code int
_item_linked.child_name '_ihm_model_representation.seq_id_end'
_item_linked.parent_name '_entity_poly_seq.num'
save_
save__ihm_model_representation.model_object_primitive
_item_description.description
; The primitive object used to model this segment.
;
_item.name '_ihm_model_representation.model_object_primitive'
_item.category_id ihm_model_representation
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail
'atomistic' .
'sphere' .
'gaussian' .
'other' .
save_
save__ihm_model_representation.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.starting_model_id'
_item.category_id ihm_model_representation
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_ihm_model_representation.starting_model_id'
_item_linked.parent_name '_ihm_starting_model_details.starting_model_id'
save_
save__ihm_model_representation.model_mode
_item_description.description
; The manner in which the segment is modeled.
;
_item.name '_ihm_model_representation.model_mode'
_item.category_id ihm_model_representation
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail
'rigid' .
'flexible' .
save_
save__ihm_model_representation.model_granularity
_item_description.description
; The level of detail at which model primitive objects are applied to the structure.
;
_item.name '_ihm_model_representation.model_granularity'
_item.category_id ihm_model_representation
_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.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.model_object_count'
_item.category_id ihm_model_representation
_item.mandatory_code no
_item_type.code int
save_
#########################
## IHM_STRUCT_ASSEMBLY ##
#########################
save_ihm_struct_assembly
_category.description
; Data items in the IHM_STRUCT_ASSEMBLY category records the
details of the structural assemblies and used in the
IHM modeling.
;
_category.id ihm_struct_assembly
_category.mandatory_code no
loop_
_category_key.name '_ihm_struct_assembly.ordinal_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.ordinal_id
_ihm_struct_assembly.assembly_id
_ihm_struct_assembly.parent_assembly_id
_ihm_struct_assembly.entity_description
_ihm_struct_assembly.entity_id
_ihm_struct_assembly.asym_id
_ihm_struct_assembly.seq_id_begin
_ihm_struct_assembly.seq_id_end
1 1 1 Nup84 1 A 1 726
2 1 1 Nup85 2 B 1 744
3 1 1 Nup120 3 C 1 1037
4 2 2 Nup133 4 D 1 1157
5 2 2 Nup145 5 E 1 712
6 3 3 Seh1 6 F 1 349
7 3 3 Sec13 7 G 1 297
#...abbreviated...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - Hierarchical assembly
;
;
loop_
_ihm_struct_assembly.ordinal_id
_ihm_struct_assembly.assembly_id
_ihm_struct_assembly.parent_assembly_id
_ihm_struct_assembly.entity_description
_ihm_struct_assembly.entity_id
_ihm_struct_assembly.asym_id
_ihm_struct_assembly.seq_id_begin
_ihm_struct_assembly.seq_id_end
1 0 0 Nup84 1 A 1 726
2 0 0 Nup85 2 B 1 744
3 0 0 Nup120 3 C 1 1037
4 0 0 Nup133 4 D 1 1157
5 0 0 Nup145 5 E 1 712
6 0 0 Seh1 6 F 1 349
7 0 0 Sec13 7 G 1 297
8 1 0 Nup84 1 A 1 726
9 1 0 Nup85 2 B 1 744
10 1 0 Nup145 5 E 1 712
11 1 0 Seh1 6 F 1 349
12 1 0 Sec13 7 G 1 297
13 2 1 Nup84 1 A 1 726
14 2 1 Nup85 2 B 1 744
#...abbreviated...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_pdbx_category_context.type CONTRIBUTED
_pdbx_category_context.category_id ihm_struct_assembly
save_
save__ihm_struct_assembly.ordinal_id
_item_description.description
; A unique identifier for the structural assembly description.
;
_item.name '_ihm_struct_assembly.ordinal_id'
_item.category_id ihm_struct_assembly
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_struct_assembly.assembly_id
_item_description.description
; An identifier for the structural assembly.
This data item will remain the same for all components
of an assembly.
;
_item.name '_ihm_struct_assembly.assembly_id'
_item.category_id ihm_struct_assembly
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_struct_assembly.parent_assembly_id
_item_description.description
; The parent of this assembly in a hierarchy.
This data item is an internal category pointer to
_ihm_struct_assembly.assembly_id
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.parent_assembly_id is the same as
_ihm_struct_assembly.assembly_id indicating a self-parent.
;
_item.name '_ihm_struct_assembly.parent_assembly_id'
_item.category_id ihm_struct_assembly
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_ihm_struct_assembly.parent_assembly_id'
_item_linked.parent_name '_ihm_struct_assembly.assembly_id'
save_
save__ihm_struct_assembly.entity_description
_item_description.description
; A text description of the molecular entity
;
_item.name '_ihm_struct_assembly.entity_description'
_item.category_id ihm_struct_assembly
_item.mandatory_code no
_item_type.code line
_item_linked.child_name '_ihm_struct_assembly.entity_description'
_item_linked.parent_name '_entity.pdbx_description'
save_
save__ihm_struct_assembly.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.entity_id'
_item.category_id ihm_struct_assembly
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ihm_struct_assembly.entity_id'
_item_linked.parent_name '_entity.id'
save_
save__ihm_struct_assembly.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.asym_id'
_item.category_id ihm_struct_assembly
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ihm_struct_assembly.asym_id'
_item_linked.parent_name '_struct_asym.id'
save_
save__ihm_struct_assembly.seq_id_begin
_item_description.description
; The starting residue index for the sequence segment of the entity instance
that is part of the assembly.
This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
;
_item.name '_ihm_struct_assembly.seq_id_begin'
_item.category_id ihm_struct_assembly
_item.mandatory_code no
_item_type.code int
_item_linked.child_name '_ihm_struct_assembly.seq_id_begin'
_item_linked.parent_name '_entity_poly_seq.num'
save_
save__ihm_struct_assembly.seq_id_end
_item_description.description
; The ending residue index for the sequence segment of the entity instance
that is part of the assembly.
This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
;
_item.name '_ihm_struct_assembly.seq_id_end'
_item.category_id ihm_struct_assembly
_item.mandatory_code no
_item_type.code int
_item_linked.child_name '_ihm_struct_assembly.seq_id_end'
_item_linked.parent_name '_entity_poly_seq.num'
save_
#################################
## IHM_STRUCT_ASSEMBLY_DETAILS ##
#################################
save_ihm_struct_assembly_details
_category.description
; Data items in the IHM_STRUCT_ASSEMBLY_DETAILS category provides
additional details regarding the structure assembly.
;
_category.id ihm_struct_assembly_details
_category.mandatory_code no
loop_
_category_key.name '_ihm_struct_assembly_details.assembly_id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_ihm_struct_assembly_details.assembly_id
_ihm_struct_assembly_details.assembly_name
_ihm_struct_assembly_details.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_details
save_
save__ihm_struct_assembly_details.assembly_id
_item_description.description
; A unique identifier for the structural assembly.
;
_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.assembly_id'
save_
save__ihm_struct_assembly_details.assembly_name
_item_description.description
; A name for the structural assembly.
;
_item.name '_ihm_struct_assembly_details.assembly_name'
_item.category_id ihm_struct_assembly_details
_item.mandatory_code no
_item_type.code line
save_
save__ihm_struct_assembly_details.assembly_description
_item_description.description
; Description of the structural assembly.
;
_item.name '_ihm_struct_assembly_details.assembly_description'
_item.category_id ihm_struct_assembly_details
_item.mandatory_code no
_item_type.code text
save_
####################################
## IHM_STRUCT_ASSEMBLY_CLASS_LIST ##
####################################
save_ihm_struct_assembly_class_list
_category.description
; Data items in the IHM_STRUCT_ASSEMBLY_CLASS_LIST 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_list
_category.mandatory_code no
loop_
_category_key.name '_ihm_struct_assembly_class_list.class_id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_ihm_struct_assembly_class_list.class_id
_ihm_struct_assembly_class_list.name
_ihm_struct_assembly_class_list.type
_ihm_struct_assembly_class_list.description
1 "TAD" "Structural Hierarchy" .
2 "CHROMATIN" "Structural Hierarchy" .
# ... abbreviated ...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_pdbx_category_context.type CONTRIBUTED
_pdbx_category_context.category_id ihm_struct_assembly_class_list
save_
save__ihm_struct_assembly_class_list.class_id
_item_description.description
; A unique identifier for the structural assembly class.
;
_item.name '_ihm_struct_assembly_class_list.class_id'
_item.category_id ihm_struct_assembly_class_list
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_struct_assembly_class_list.name
_item_description.description
; A user provided name for the class.
;
_item.name '_ihm_struct_assembly_class_list.name'
_item.category_id ihm_struct_assembly_class_list
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case
"TAD"
"Chromatin"
save_
save__ihm_struct_assembly_class_list.type
_item_description.description
; The type of classifier.
;
_item.name '_ihm_struct_assembly_class_list.type'
_item.category_id ihm_struct_assembly_class_list
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
"Structural Hierarchy"
"Functional"
"Other"
save_
save__ihm_struct_assembly_class_list.description
_item_description.description
; Additional description regarding the class.
;
_item.name '_ihm_struct_assembly_class_list.description'
_item.category_id ihm_struct_assembly_class_list
_item.mandatory_code no
_item_type.code text
save_
###############################
## IHM_STRUCT_ASSEMBLY_CLASS ##
###############################
save_ihm_struct_assembly_class
_category.description
; Data items in the IHM_STRUCT_ASSEMBLY_CLASS 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
_category.mandatory_code no
loop_
_category_key.name '_ihm_struct_assembly_class.ordinal_id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_ihm_struct_assembly_class.ordinal_id
_ihm_struct_assembly_class.class_id
_ihm_struct_assembly_class.assembly_id
1 1 1
2 1 2
3 1 3
4 2 4
# ... abbreviated ...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_pdbx_category_context.type CONTRIBUTED
_pdbx_category_context.category_id ihm_struct_assembly_class
save_
save__ihm_struct_assembly_class.ordinal_id
_item_description.description
; A unique identifier for the category.
;
_item.name '_ihm_struct_assembly_class.ordinal_id'
_item.category_id ihm_struct_assembly_class
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_struct_assembly_class.class_id
_item_description.description
; An identifier for the structural assembly class.
This data item is a pointer to _ihm_struct_assembly_class_list.class_id
in the IHM_STRUCT_ASSEMBLY_CLASS_LIST category.
;
_item.name '_ihm_struct_assembly_class.class_id'
_item.category_id ihm_struct_assembly_class
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_ihm_struct_assembly_class.class_id'
_item_linked.parent_name '_ihm_struct_assembly_class_list.class_id'
save_
save__ihm_struct_assembly_class.assembly_id
_item_description.description
; An identifier for the structural assembly.
This data item is a pointer to _ihm_struct_assembly.assembly_id
in the IHM_STRUCT_ASSEMBLY category.
;
_item.name '_ihm_struct_assembly_class.assembly_id'
_item.category_id ihm_struct_assembly_class
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_ihm_struct_assembly_class.assembly_id'
_item_linked.parent_name '_ihm_struct_assembly.assembly_id'
save_
#############################
## IHM_MODELING_PROTOCOL ##
#############################
save_ihm_modeling_protocol
_category.description
; Data items in the IHM_MODELING_PROTOCOL category records the
step-wise details of the integrative modeling workflow.
;
_category.id ihm_modeling_protocol
_category.mandatory_code no
loop_
_category_key.name '_ihm_modeling_protocol.ordinal_id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
_ihm_modeling_protocol.ordinal_id
_ihm_modeling_protocol.protocol_id
_ihm_modeling_protocol.step_id
_ihm_modeling_protocol.struct_assembly_id
_ihm_modeling_protocol.dataset_group_id
_ihm_modeling_protocol.struct_assembly_description
_ihm_modeling_protocol.protocol_name
_ihm_modeling_protocol.step_name
_ihm_modeling_protocol.step_method
_ihm_modeling_protocol.num_models_begin
_ihm_modeling_protocol.num_models_end
_ihm_modeling_protocol.multi_scale_flag
_ihm_modeling_protocol.multi_state_flag
_ihm_modeling_protocol.ordered_flag
_ihm_modeling_protocol.ensemble_flag
1 1 1 1 1 'Nup84 sub-complex' 'Multi-scale modeling' 'Sampling' 'Replica exchange monte carlo' 0 7500 'YES' 'NO' 'NO' 'NO'
2 1 2 1 2 'Nup84 sub-complex' 'Multi-scale modeling' 'Sampling' 'Replica exchange monte carlo' 7500 15000 'YES' 'NO' 'NO' 'NO'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 -
;
;
_ihm_modeling_protocol.ordinal_id
_ihm_modeling_protocol.protocol_id
_ihm_modeling_protocol.step_id
_ihm_modeling_protocol.struct_assembly_id
_ihm_modeling_protocol.dataset_group_id
_ihm_modeling_protocol.struct_assembly_description
_ihm_modeling_protocol.protocol_name
_ihm_modeling_protocol.step_name
_ihm_modeling_protocol.step_method
_ihm_modeling_protocol.num_models_begin
_ihm_modeling_protocol.num_models_end
_ihm_modeling_protocol.multi_scale_flag
_ihm_modeling_protocol.multi_state_flag
_ihm_modeling_protocol.ordered_flag
_ihm_modeling_protocol.ensemble_flag
1 1 1 1 1 'PhoQ' 'Multi-state modeling' 'Sampling' 'Monte carlo' 0 5000 'NO' 'YES' 'NO' 'YES'
2 1 1 2 1 'PhoQ' 'Multi-state modeling' 'Sampling' 'Monte carlo' 0 5000 'NO' 'YES' 'NO' 'YES'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_pdbx_category_context.type CONTRIBUTED
_pdbx_category_context.category_id ihm_modeling_protocol
save_
save__ihm_modeling_protocol.ordinal_id
_item_description.description
; A unique identifier for the modeling protocol/step combination.
;
_item.name '_ihm_modeling_protocol.ordinal_id'
_item.category_id ihm_modeling_protocol
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_modeling_protocol.protocol_id
_item_description.description
; An index for the modeling protocol carried out.
;
_item.name '_ihm_modeling_protocol.protocol_id'
_item.category_id ihm_modeling_protocol
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_modeling_protocol.step_id
_item_description.description
; An index for a particular step within the modeling protocol.
;
_item.name '_ihm_modeling_protocol.step_id'
_item.category_id ihm_modeling_protocol
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_modeling_protocol.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.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.struct_assembly_id'
_item.category_id ihm_modeling_protocol
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_ihm_modeling_protocol.struct_assembly_id'
_item_linked.parent_name '_ihm_struct_assembly.assembly_id'
_item_default.value 1
save_
save__ihm_modeling_protocol.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.group_id in the
IHM_DATASET_GROUP category.
;
_item.name '_ihm_modeling_protocol.dataset_group_id'
_item.category_id ihm_modeling_protocol
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_ihm_modeling_protocol.dataset_group_id'
_item_linked.parent_name '_ihm_dataset_group.group_id'
save_
save__ihm_modeling_protocol.struct_assembly_description
_item_description.description
; A textual description of the structural assembly being modeled.
;
_item.name '_ihm_modeling_protocol.struct_assembly_description'
_item.category_id ihm_modeling_protocol
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'Nup84 sub-complex'
'PhoQ'
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'
'Multi-state modeling'
'Multi-scale time-ordered modeling'
save_
save__ihm_modeling_protocol.step_name
_item_description.description
; The name or type of the modeling step.
;
_item.name '_ihm_modeling_protocol.step_name'
_item.category_id ihm_modeling_protocol
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'Sampling/Scoring'
'Refinement'
save_
save__ihm_modeling_protocol.step_method
_item_description.description
; Description of the method involved in the modeling step.
;
_item.name '_ihm_modeling_protocol.step_method'
_item.category_id ihm_modeling_protocol
_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.num_models_begin
_item_description.description
; The number of models in the beginning of the step.
;
_item.name '_ihm_modeling_protocol.num_models_begin'
_item.category_id ihm_modeling_protocol
_item.mandatory_code no
_item_type.code int
save_
save__ihm_modeling_protocol.num_models_end
_item_description.description
; The number of models at the end of the step.
;
_item.name '_ihm_modeling_protocol.num_models_end'
_item.category_id ihm_modeling_protocol
_item.mandatory_code no
_item_type.code int
save_
save__ihm_modeling_protocol.multi_scale_flag
_item_description.description
; A flag to indicate if the modeling is multi scale.
;
_item.name '_ihm_modeling_protocol.multi_scale_flag'
_item.category_id ihm_modeling_protocol
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail
'YES' .
'NO' .
save_
save__ihm_modeling_protocol.multi_state_flag
_item_description.description
; A flag to indicate if the modeling is multi state.
;
_item.name '_ihm_modeling_protocol.multi_state_flag'
_item.category_id ihm_modeling_protocol
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail
'YES' .
'NO' .
save_
save__ihm_modeling_protocol.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.ordered_flag'
_item.category_id ihm_modeling_protocol
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail
'YES' .
'NO' .
save_
save__ihm_modeling_protocol.ensemble_flag
_item_description.description
; A flag to indicate if the modeling involves an ensemble.
;
_item.name '_ihm_modeling_protocol.ensemble_flag'
_item.category_id ihm_modeling_protocol
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail
'YES' .
'NO' .
save_
save__ihm_modeling_protocol.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.script_file_id'
_item.category_id ihm_modeling_protocol
_item.mandatory_code no
_item_type.code int
_item_linked.child_name '_ihm_modeling_protocol.script_file_id'
_item_linked.parent_name '_ihm_external_files.id'
save_
save__ihm_modeling_protocol.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.software_id'
_item.category_id ihm_modeling_protocol
_item.mandatory_code no
_item_type.code int
_item_linked.child_name '_ihm_modeling_protocol.software_id'
_item_linked.parent_name '_software.pdbx_ordinal'
save_
###########################
## IHM_MULTI_STATE_MODELING
###########################
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
loop_
_category_key.name '_ihm_multi_state_modeling.ordinal_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.ordinal_id
_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.model_group_id
_ihm_multi_state_modeling.experiment_type
_ihm_multi_state_modeling.details
1 1 1 0.5 'conformational change' 'open' 1 'Fraction of bulk' 'open state ensemble 1'
2 2 1 0.5 'conformational change' 'closed' 2 'Fraction of bulk' 'closed state ensemble 2'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - ligand binding
;
;
loop_
_ihm_multi_state_modeling.ordinal_id
_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.model_group_id
_ihm_multi_state_modeling.experiment_type
_ihm_multi_state_modeling.details
1 1 1 0.25 'ligand binding' 'unbound' 1 'Fraction of bulk' 'unbound'
2 2 1 0.75 'ligand binding' 'bound' 2 'Fraction of bulk' 'bound to heme'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 3 - complex formation
;
;
loop_
_ihm_multi_state_modeling.ordinal_id
_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.model_group_id
_ihm_multi_state_modeling.experiment_type
_ihm_multi_state_modeling.details
1 1 1 . 'complex formation' 'unbound' 1 'Fraction of bulk' 'unbound molecule 1'
2 2 1 . 'complex formation' 'unbound' 2 'Fraction of bulk' 'unbound molecule 2'
3 3 1 . 'complex formation' 'bound' 3 '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.ordinal_id
_item_description.description
; A unique identifier for the multiple states being described.
;
_item.name '_ihm_multi_state_modeling.ordinal_id'
_item.category_id ihm_multi_state_modeling
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_multi_state_modeling.state_id
_item_description.description
; An identifier for the 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.
If the states do not need to be grouped into collections, then
_ihm_multi_state_modeling.state_group_id is the same as
_ihm_multi_state_modeling.state_id.
;
_item.name '_ihm_multi_state_modeling.state_group_id'
_item.category_id ihm_multi_state_modeling
_item.mandatory_code yes
_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 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 yes
_item_type.code line
loop_
_item_examples.case
'open'
'closed'
'bound'
'unbound'
'active'
'inactive'
'relaxed'
'tensed'
save_
save__ihm_multi_state_modeling.model_group_id
_item_description.description
; The model group id corresponding to the particular state in the multi-state model.
This data item is a pointer to _ihm_model_list.model_group_id in the
IHM_MODEL_LIST category.
If there is only a single model corresponding to a particular state, then the
_ihm_model_list.model_group_id is the same as the _ihm_model_list.model_id.
;
_item.name '_ihm_multi_state_modeling.model_group_id'
_item.category_id ihm_multi_state_modeling
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_ihm_multi_state_modeling.model_group_id'
_item_linked.parent_name '_ihm_model_list.model_group_id'
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_
##########################
## IHM_ORDERED_ENSEMBLE ##
##########################
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 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_list.model_group_id in the
IHM_MODEL_LIST category.
If the node involves a single model instead of a collection of models,
then the _ihm_model_list.model_group_id is the same as the _ihm_model_list.model_id.
;
_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_list.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_list.model_group_id in the
IHM_MODEL_LIST category.
If the node involves a single model instead of a collection of models,
then the _ihm_model_list.model_group_id is the same as the _ihm_model_list.model_id.
;
_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_list.model_group_id'
save_
############################
## IHM_MODELING_POST_PROCESS
############################
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
loop_
_category_key.name '_ihm_modeling_post_process.id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
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.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.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.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.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.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.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 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 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_
#######################
## IHM_ENSEMBLE_INFO ##
#######################
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
loop_
_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_list.model_group_id
in the IHM_MODEL_LIST 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_list.model_group_id'
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)'
'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_
#################
## IHM_MODEL_LIST
#################
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
loop_
_category_key.name '_ihm_model_list.ordinal_id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_ihm_model_list.ordinal_id
_ihm_model_list.model_id
_ihm_model_list.model_group_id
_ihm_model_list.model_name
_ihm_model_list.model_group_name
_ihm_model_list.assembly_id
_ihm_model_list.protocol_id
_ihm_model_list.representation_id
1 1 1 'Best scoring model' 'ensemble1' 1 1 1
2 2 1 '2nd Best scoring model' 'ensemble1' 1 1 1
3 3 1 '3rd Best scoring model' 'ensemble1' 1 1 1
4 4 1 '4th Best scoring model' 'ensemble1' 1 1 1
5 5 1 '5th Best scoring model' 'ensemble1' 1 1 1
6 6 2 'Best scoring model' 'ensemble2' 1 1 1
7 7 2 '2nd Best scoring model' 'ensemble2' 1 1 1
8 8 2 '3rd Best scoring model' 'ensemble2' 1 1 1
9 9 2 '4th Best scoring model' 'ensemble2' 1 1 1
10 10 2 '5th Best scoring model' 'ensemble2' 1 1 1
# ... abbreviated ...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 -
;
;
loop_
_ihm_model_list.ordinal_id
_ihm_model_list.model_id
_ihm_model_list.model_group_id
_ihm_model_list.model_group_name
_ihm_model_list.assembly_id
_ihm_model_list.protocol_id
_ihm_model_list.representation_id
1 1 1 'open state' 1 1 1
2 2 1 'open state' 1 1 1
3 3 1 'open state' 1 1 1
4 4 1 'open state' 1 1 1
5 5 1 'open state' 1 1 1
6 6 2 'closed state' 1 1 1
7 7 2 'closed state' 1 1 1
8 8 2 'closed state' 1 1 1
9 9 2 'closed state' 1 1 1
10 10 2 'closed state' 1 1 1
# ... abbreviated ...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 3 -
;
;
loop_
_ihm_model_list.ordinal_id
_ihm_model_list.model_id
_ihm_model_list.model_group_id
_ihm_model_list.model_group_name
_ihm_model_list.assembly_id
_ihm_model_list.protocol_id
_ihm_model_list.representation_id
1 1 1 'Bound state ensemble 1' 1 1 1
2 2 1 'Bound state ensemble 1' 1 1 1
3 3 1 'Bound state ensemble 1' 1 1 1
4 4 1 'Bound state ensemble 1' 1 1 1
5 5 1 'Bound state ensemble 1' 1 1 1
6 6 2 'Unbound state ensemble 2' 2 1 2
7 7 2 'Unbound state ensemble 2' 2 1 2
8 8 2 'Unbound state ensemble 2' 2 1 2
9 9 2 'Unbound state ensemble 2' 2 1 2
10 10 2 'Unbound state ensemble 2' 2 1 2
# ... abbreviated ...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 4 - Multi-scale, multi-state and time-ordered ensemble
;
;
loop_
_ihm_model_list.ordinal_id
_ihm_model_list.model_id
_ihm_model_list.model_group_id
_ihm_model_list.model_name
_ihm_model_list.model_group_name
_ihm_model_list.assembly_id
_ihm_model_list.protocol_id
_ihm_model_list.representation_id
1 1 1 'Best scoring model' 'Open state' 1 1 1
2 2 1 '2nd Best scoring model' 'Open state' 1 1 1
3 3 2 'Best scoring model' 'Closed state' 1 1 1
4 4 2 '2nd Best scoring model' 'Closed state' 1 1 1
5 1 3 'Best scoring model' 'Time step 1' 1 1 1
6 2 3 '2nd Best scoring model' 'Time step 1' 1 1 1
7 3 3 '3rd Best scoring model' 'Time step 1' 1 1 1
8 4 3 '4th Best scoring model' 'Time step 1' 1 1 1
9 5 4 'Best scoring model' 'Open state' 1 1 1
10 6 4 '2nd Best scoring model' 'Open state' 1 1 1
11 7 5 'Best scoring model' 'Closed state' 1 1 1
12 8 5 '2nd Best scoring model' 'Closed state' 1 1 1
13 5 6 'Best scoring model' 'Time step 2' 1 1 1
14 6 6 '2nd Best scoring model' 'Time step 2' 1 1 1
15 7 6 '3rd Best scoring model' 'Time step 2' 1 1 1
16 8 6 '4th Best scoring model' '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.ordinal_id
_item_description.description
; A unique identifier for the model / model group combination.
;
_item.name '_ihm_model_list.ordinal_id'
_item.category_id ihm_model_list
_item.mandatory_code yes
_item_type.code int
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_group_id
_item_description.description
; An identifier to group structural models into collections or sets.
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_list 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.
If the models do not need to be grouped into collections, then the
_ihm_model_list.model_group_id is the same as _ihm_model_list.model_id.
;
_item.name '_ihm_model_list.model_group_id'
_item.category_id ihm_model_list
_item.mandatory_code yes
_item_type.code int
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.model_group_name
_item_description.description
; A decsriptive name for the model group.
;
_item.name '_ihm_model_list.model_group_name'
_item.category_id ihm_model_list
_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_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.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.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.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.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.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.representation_id'
save_
##############################
## IHM_MODEL_REPRESENTATIVE ##
##############################
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
loop_
_category_key.name '_ihm_model_representative.id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
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_list.model_group_id in the
IHM_MODEL_LIST 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_list.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 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_
###############
## ATOM_SITE ##
###############
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_
######################
## IHM_DATASET_LIST ##
######################
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'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
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'
'SAS data'
'CX-MS data'
'Mass Spectrometry data'
'EPR data'
'H/D exchange data'
'Single molecule 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'
'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_
#######################
## IHM_DATASET_GROUP ##
#######################
save_ihm_dataset_group
_category.description
; Category provides a mechanism to group datasets.
;
_category.id ihm_dataset_group
_category.mandatory_code no
_category_key.name '_ihm_dataset_group.ordinal_id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
loop_
_ihm_dataset_group.ordinal_id
_ihm_dataset_group.group_id
_ihm_dataset_group.dataset_list_id
1 1 1
2 1 2
3 1 3
4 2 3
5 2 4
6 2 5
# ... abbreviated ...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_pdbx_category_context.type CONTRIBUTED
_pdbx_category_context.category_id ihm_dataset_group
save_
save__ihm_dataset_group.ordinal_id
_item_description.description
; A unique identifier for the entry.
;
_item.name '_ihm_dataset_group.ordinal_id'
_item.category_id ihm_dataset_group
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_dataset_group.group_id
_item_description.description
; An identifier for the dataset group.
;
_item.name '_ihm_dataset_group.group_id'
_item.category_id ihm_dataset_group
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_dataset_group.dataset_list_id
_item_description.description
; An identifier to the dataset. This data item is a pointer to
_ihm_dataset_list.id in the IHM_DATASET_LIST category.
;
_item.name '_ihm_dataset_group.dataset_list_id'
_item.category_id ihm_dataset_group
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_ihm_dataset_group.dataset_list_id'
_item_linked.parent_name '_ihm_dataset_list.id'
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_
##########################
## IHM_RELATED_DATASETS ##
##########################
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
_category_key.name '_ihm_related_datasets.ordinal_id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
loop_
_ihm_related_datasets.ordinal_id
_ihm_related_datasets.dataset_list_id_derived
_ihm_related_datasets.dataset_list_id_primary
1 1 5
2 2 6
3 3 7
4 4 8
# ... abbreviated ... #
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_pdbx_category_context.type CONTRIBUTED
_pdbx_category_context.category_id ihm_related_datasets
save_
save__ihm_related_datasets.ordinal_id
_item_description.description
; A unique identifier for the entry.
;
_item.name '_ihm_related_datasets.ordinal_id'
_item.category_id ihm_related_datasets
_item.mandatory_code yes
_item_type.code int
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_
######################################
## IHM_DATASET_RELATED_DB_REFERENCE ##
######################################
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'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
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'
'BMRB'
'EMDB'
'EMPIAR'
'SASBDB'
'PRIDE'
'MODEL ARCHIVE'
'MASSIVE'
'BioGRID'
'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
loop_
_item_examples.case
'Structural Analysis of a Prokaryotic Ribosome Using a Novel Amidinating Cross-Linker and Mass Spectrometry'
save_
#################################
## IHM_EXTERNAL_REFERENCE_INFO ##
#################################
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
loop_
_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_
########################
## IHM_EXTERNAL_FILES ##
########################
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 yes
_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
; Textual description of what the external file is.
;
_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_
####################################
## IHM_DATASET_EXTERNAL_REFERENCE ##
####################################
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'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
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_
####################################
## IHM_LOCALIZATION_DENSITY_FILES ##
####################################
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
loop_
_category_key.name '_ihm_localization_density_files.id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
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.seq_id_begin
_ihm_localization_density_files.seq_id_end
1 12 1 1 A 1 726
2 13 1 2 B 1 744
3 14 1 3 C 1 1037
# ...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 yes
_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.seq_id_begin
_item_description.description
; The leading sequence index corresponding to this localization density.
This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
;
_item.name '_ihm_localization_density_files.seq_id_begin'
_item.category_id ihm_localization_density_files
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_ihm_localization_density_files.seq_id_begin'
_item_linked.parent_name '_entity_poly_seq.num'
save_
save__ihm_localization_density_files.seq_id_end
_item_description.description
; The trailing sequence index corresponding to this localization density.
This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
;
_item.name '_ihm_localization_density_files.seq_id_end'
_item.category_id ihm_localization_density_files
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_ihm_localization_density_files.seq_id_end'
_item_linked.parent_name '_entity_poly_seq.num'
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 yes
_item_type.code code
_item_linked.child_name '_ihm_localization_density_files.asym_id'
_item_linked.parent_name '_struct_asym.id'
save_
#####################################
## IHM_PREDICTED_CONTACT_RESTRAINT ##
#####################################
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
loop_
_category_key.name '_ihm_predicted_contact_restraint.id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
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.atom_id_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.atom_id_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
_item_linked.child_name '_ihm_predicted_contact_restraint.entity_description_1'
_item_linked.parent_name '_entity.pdbx_description'
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
_item_linked.child_name '_ihm_predicted_contact_restraint.entity_description_2'
_item_linked.parent_name '_entity.pdbx_description'
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_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_linked.child_name '_ihm_predicted_contact_restraint.entity_id_2'
_item_linked.parent_name '_entity_poly_seq.entity_id'