########################################################################### # # File: mmcif_iims-def-2.dic # # PDB Extension Dictionary for 3-Dimensional # Electron Microscopy # # Definition Section 2 # # ########################################################################### ## ### # Please note the data items listed below are not for the PDB # but are intended solely for the EM database # _em_entity_assembly.ebi_organism_scientific # _em_entity_assembly.ebi_organism_common # _em_entity_assembly.ebi_strain # _em_entity_assembly.ebi_tissue # _em_entity_assembly.ebi_cell # _em_entity_assembly.ebi_organelle # _em_entity_assembly.ebi_cellular_location # _em_entity_assembly.ebi_engineered # _em_entity_assembly.ebi_expression_system # _em_entity_assembly.ebi_expression_system_plasmid ### # # categories # # EM_ASSEMBLY # _em_assembly.id # _em_assembly.entry_id # _em_assembly.name # _em_assembly.aggregation_state # _em_assembly.composition # _em_assembly.num_components # _em_assembly.mol_wt_exp # _em_assembly.mol_wt_theo # _em_assembly.mol_wt_method # _em_assembly.details # EM_ENTITY_ASSEMBLY # _em_entity_assembly.id # _em_entity_assembly.assembly_id # _em_entity_assembly.type # _em_entity_assembly.name # _em_entity_assembly.details # _em_entity_assembly.go_id # _em_entity_assembly.ipr_id # _em_entity_assembly.synonym # EM_ENTITY_ASSEMBLY_LIST # _em_entity_assembly_list.id # _em_entity_assembly_list.entity_id # _em_entity_assembly_list.entity_assembly_id # _em_entity_assembly_list.oligomeric_details # _em_entity_assembly_list.number_of_copies # EM_VIRUS_ENTITY # _em_virus_entity.id # _em_virus_entity.virus_host_category # _em_virus_entity.virus_host_species # _em_virus_entity.virus_host_growth_cell # _em_virus_entity.virus_type # _em_virus_entity.virus_isolate # _em_virus_entity.ictvdb_id # _em_virus_entity.entity_assembly_id # _em_virus_entity.enveloped # _em_virus_entity.empty # EM_ICOS_VIRUS_SHELLS # _em_icos_virus_shells.virus_entity_id # _em_icos_virus_shells.id # _em_icos_virus_shells.shell_diameter # _em_icos_virus_shells.triangulation_num # EM_SAMPLE_PREPARATION # _em_sample_preparation.entry_id # _em_sample_preparation.id # _em_sample_preparation.ph # _em_sample_preparation.buffer_id # _em_sample_preparation.sample_concentration # _em_sample_preparation.2d_crystal_grow_id # _em_sample_preparation.support_id # EM_SAMPLE_SUPPORT # _em_sample_support.id # _em_sample_support.film_material # _em_sample_support.method # _em_sample_support.grid_material # _em_sample_support.grid_mesh_size # _em_sample_support.grid_type # _em_sample_support.pretreatment # _em_sample_support.details # _em_sample_support.citation_id # EM_2D_CRYSTAL_GROW # _em_2d_crystal_grow.id # _em_2d_crystal_grow.method # _em_2d_crystal_grow.apparatus # _em_2d_crystal_grow.atmosphere # _em_2d_crystal_grow.pH # _em_2d_crystal_grow.temp # _em_2d_crystal_grow.time # _em_2d_crystal_grow.buffer_id # _em_2d_crystal_grow.details # _em_2d_crystal_grow.number_2d_crystals # _em_2d_crystal_grow.mean_2d_crystal_size # _em_2d_crystal_grow.citation_id # EM_BUFFER # _em_buffer.id # _em_buffer.name # _em_buffer.details # EM_BUFFER_COMPONENTS # _em_buffer_components.id # _em_buffer_components.buffer_id # _em_buffer_components.name # _em_buffer_components.volume # _em_buffer_components.conc # _em_buffer_components.details # EM_VITRIFICATION # _em_vitrification.entry_id # _em_vitrification.id # _em_vitrification.sample_preparation_id # _em_vitrification.cryogen_name # _em_vitrification.humidity # _em_vitrification.temp # _em_vitrification.instrument # _em_vitrification.method # _em_vitrification.time_resolved_state # _em_vitrification.citation_id # _em_vitrification.details # EM_IMAGING # _em_imaging.entry_id # _em_imaging.id # _em_imaging.sample_support_id # _em_imaging.detector_id # _em_imaging.scans_id # _em_imaging.microscope_model # _em_imaging.specimen_holder_type # _em_imaging.specimen_holder_model # _em_imaging.details # _em_imaging.date # _em_imaging.accelerating_voltage # _em_imaging.illumination_mode # _em_imaging.mode # _em_imaging.nominal_cs # _em_imaging.nominal_defocus_min # _em_imaging.nominal_defocus_max # _em_imaging.tilt_angle_min # _em_imaging.tilt_angle_max # _em_imaging.nominal_magnification # _em_imaging.calibrated_magnification # _em_imaging.electron_source # _em_imaging.electron_dose # _em_imaging.energy_filter # _em_imaging.energy_window # _em_imaging.citation_id # _em_imaging.temperature # _em_imaging.detector_distance # _em_imaging.recording_temperature_minimum # _em_imaging.recording_temperature_maximum # EM_DETECTOR # _em_detector.entry_id # _em_detector.id # _em_detector.details # _em_detector.type # _em_detector.detective_quantum_efficiency # EM_IMAGE_SCANS # _em_image_scans.entry_id # _em_image_scans.id # _em_image_scans.number_digital_images # _em_image_scans.details # _em_image_scans.scanner_model # _em_image_scans.sampling_size # _em_image_scans.od_range # _em_image_scans.quant_bit_size # _em_image_scans.citation_id # EM_2D_PROJECTION_SELECTION # _em_2d_projection_selection.entry_id # _em_2d_projection_selection.num_particles # _em_2d_projection_selection.software_name # _em_2d_projection_selection.method # _em_2d_projection_selection.details # _em_2d_projection_selection.citation_id # EM_EULER_ANGLE_DISTRIBUTION # _em_euler_angle_distribution.id # _em_euler_angle_distribution.entry_id # _em_euler_angle_distribution.details # _em_euler_angle_distribution.alpha # _em_euler_angle_distribution.beta # _em_euler_angle_distribution.gamma # EM_3D_RECONSTRUCTION # _em_3d_reconstruction.entry_id # _em_3d_reconstruction.id # _em_3d_reconstruction.method # _em_3d_reconstruction.citation_id # _em_3d_reconstruction.details # _em_3d_reconstruction.resolution # _em_3d_reconstruction.resolution_method # _em_3d_reconstruction.magnification_calibration # _em_3d_reconstruction.ctf_correction_method # _em_3d_reconstruction.nominal_pixel_size # _em_3d_reconstruction.actual_pixel_size # EM_3D_FITTING # _em_3d_fitting.id # _em_3d_fitting.entry_id # _em_3d_fitting.method # _em_3d_fitting.target_criteria # _em_3d_fitting.software_name # _em_3d_fitting.details # _em_3d_fitting.overall_b_value # _em_3d_fitting.ref_space # _em_3d_fitting.ref_protocol # EM_3D_FITTING_LIST # _em_3d_fitting_list.id # _em_3d_fitting_list.3d_fitting_id # _em_3d_fitting_list.pdb_entry_id # _em_3d_fitting_list.pdb_chain_id ################# ## EM_ASSEMBLY ## ################# save_em_assembly _category.description ; Data items in the EM_ASSEMBLY category record details about the type of complex assembly that describes the nature of the sample studied. ; _category.id em_assembly _category.mandatory_code no loop_ _category_key.name '_em_assembly.id' '_em_assembly.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_assembly.id 1 _em_assembly.entry_id 1DYL _em_assembly.name virus _em_assembly.aggregation_state icosahedral _em_assembly.composition virus _em_assembly.num_components 1 _em_assembly.mol_wt_exp . _em_assembly.mol_wt_theo . _em_assembly.mol_wt_method . _em_assembly.details . ; save_ save__em_assembly.id _item_description.description ; The value of _em_assembly.id must uniquely identify a collection of observed complexes. ; _item.name '_em_assembly.id' _item.category_id em_assembly _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_entity_assembly.assembly_id' _item_linked.parent_name '_em_assembly.id' save_ save__em_assembly.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_assembly.entry_id' _item.category_id em_assembly _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_assembly.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_assembly.name _item_description.description ; The name of the assembly of observed complexes. ; _item.name '_em_assembly.name' _item.category_id em_assembly _item.mandatory_code no _item_type.code line save_ save__em_assembly.aggregation_state _item_description.description ; A description of the aggregation state of the assembly. ; _item.name '_em_assembly.aggregation_state' _item.category_id em_assembly _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'SINGLE PARTICLE' 'INDIVIDUAL STRUCTURE' '2D-CRYSTAL' ICOSAHEDRAL HELICAL FILAMENT 'HELICAL FILAMENTS' TISSUE save_ save__em_assembly.composition _item_description.description ; The known composition of the assembly. ; _item.name '_em_assembly.composition' _item.category_id em_assembly _item.mandatory_code no _item_type.code line save_ save__em_assembly.num_components _item_description.description ; The number of components of the biological assembly. ; _item.name '_em_assembly.num_components' _item.category_id em_assembly _item.mandatory_code no _item_type.code int save_ save__em_assembly.mol_wt_exp _item_description.description ; The value (in megadaltons) of the experimentally determined molecular weight of the assembly. ; _item.name '_em_assembly.mol_wt_exp' _item.category_id em_assembly _item.mandatory_code no _item_type.code float _item_units.code megadaltons save_ save__em_assembly.mol_wt_theo _item_description.description ; The value (in megadaltons) of the theoretically determined molecular weight of the assembly. ; _item.name '_em_assembly.mol_wt_theo' _item.category_id em_assembly _item.mandatory_code no _item_type.code float _item_units.code megadaltons save_ save__em_assembly.mol_wt_method _item_description.description ; The method used in determining the molecular weight. ; _item.name '_em_assembly.mol_wt_method' _item.category_id em_assembly _item.mandatory_code no _item_type.code text save_ save__em_assembly.details _item_description.description ; A description of any additional details describing the observed sample. ; _item.name '_em_assembly.details' _item.category_id em_assembly _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; This structure was preferentially oriented (end-on)on the grid. ; ; The structure was monodisperse. ; save_ ######################## ## EM_ENTITY_ASSEMBLY ## ######################## save_em_entity_assembly _category.description ; Data items in the EM_ENTITY_ASSEMBLY category record details about each component of the complex. ; _category.id em_entity_assembly _category.mandatory_code no loop_ _category_key.name '_em_entity_assembly.id' '_em_entity_assembly.assembly_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_entity_assembly.id 1 _em_entity_assembly.assembly_id 1 _em_entity_assembly.type VIRUS ; save_ save__em_entity_assembly.id _item_description.description ; The value of _em_entity_assembly.id must uniquely identify each of the components of the complex. ; _item.name '_em_entity_assembly.id' _item.category_id em_entity_assembly _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_virus_entity.entity_assembly_id' _item_linked.parent_name '_em_entity_assembly.id' save_ save__em_entity_assembly.assembly_id _item_description.description ; This data item is a pointer to _em_assembly.id in the ASSEMBLY category. ; _item.name '_em_entity_assembly.assembly_id' _item.category_id em_entity_assembly _item.mandatory_code yes _item_type.code code save_ save__em_entity_assembly.type _item_description.description ; A description of types of components of the assembly of the biological structure. ; _item.name '_em_entity_assembly.type' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value VIRUS PROTEIN 'NUCLEIC ACID' LIGAND LABEL 'CELLULAR COMPONENT' save_ save__em_entity_assembly.name _item_description.description ; The name of the component of the observed assembly. ; _item.name '_em_entity_assembly.name' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text save_ save__em_entity_assembly.details _item_description.description ; Additional details about the component. ; _item.name '_em_entity_assembly.details' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text save_ save__em_entity_assembly.ebi_organism_scientific _item_description.description ; The species of the natural organism from which the component was obtained. ; _item.name '_em_entity_assembly.ebi_organism_scientific' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text save_ save__em_entity_assembly.ebi_organism_common _item_description.description ; The common name of the species of the natural organism from which the component was obtained. ; _item.name '_em_entity_assembly.ebi_organism_common' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text save_ save__em_entity_assembly.ebi_strain _item_description.description ; The strain of the natural organism from which the component was obtained, if relevant. ; _item.name '_em_entity_assembly.ebi_strain' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'DH5a' 'BMH 71-18' save_ save__em_entity_assembly.ebi_tissue _item_description.description ; The tissue of the natural organism from which the component was obtained. ; _item.name '_em_entity_assembly.ebi_tissue' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'heart' 'liver' 'eye lens' save_ save__em_entity_assembly.ebi_cell _item_description.description ; The cell from which the component was obtained. ; _item.name '_em_entity_assembly.ebi_cell' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'CHO' 'HELA' '3T3' save_ save__em_entity_assembly.ebi_organelle _item_description.description ; The organelle from which the component was obtained. ; _item.name '_em_entity_assembly.ebi_organelle' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'golgi' 'mitochondrion' 'cytoskeleton' save_ save__em_entity_assembly.ebi_cellular_location _item_description.description ; The cellular location of the component. ; _item.name '_em_entity_assembly.ebi_cellular_location' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'cytoplasm' 'endoplasmic reticulum' 'plasma membrane' save_ save__em_entity_assembly.ebi_engineered _item_description.description ; A flag to indicate whether the component is engineered. ; _item.name '_em_entity_assembly.ebi_engineered' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value YES NO save_ save__em_entity_assembly.ebi_expression_system _item_description.description ; The expression system used to produce the component. ; _item.name '_em_entity_assembly.ebi_expression_system' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'eschericia coli' 'saccharomyces cerevisiae' save_ save__em_entity_assembly.ebi_expression_system_plasmid _item_description.description ; The plasmid used in the expression system used to produce the component. ; _item.name '_em_entity_assembly.ebi_expression_system_plasmid' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'pBR322' 'pMB9' save_ save__em_entity_assembly.go_id _item_description.description ; The Gene Ontology (GO) identifier for the component. The GO id is the appropriate identifier used by the Gene Ontology Consortium. Reference: Nature Genetics vol 25:25-29 (2000). ; _item.name '_em_entity_assembly.go_id' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'GO:0005876' 'GO:0015630' save_ save__em_entity_assembly.ipr_id _item_description.description ; The InterPro (IPR) identifier for the component. The IPR id is the appropriate identifier used by the Interpro Resource. Reference: Nucleic Acid Research vol 29(1):37-40(2001). ; _item.name '_em_entity_assembly.ipr_id' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line loop_ _item_examples.case '001304' '002353' save_ save__em_entity_assembly.synonym _item_description.description ; Alternative name of the component. ; _item.name '_em_entity_assembly.synonym' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line _item_examples.case 'FADV-1' save_ ############################# ## EM_ENTITY_ASSEMBLY_LIST ## ############################# save_em_entity_assembly_list _category.description ; Data items in the EM_ENTITY_ASSEMBLY_LIST category record details of the structural elements in each component. ; _category.id em_entity_assembly_list _category.mandatory_code no loop_ _category_key.name '_em_entity_assembly_list.entity_assembly_id' '_em_entity_assembly_list.id' '_em_entity_assembly_list.entity_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - microtubule ; ; loop_ _em_entity_assembly_list.entity_assembly_id _em_entity_assembly_list.id _em_entity_assembly_list.entity_id _em_entity_assembly_list.oligomeric_details _em_entity_assembly_list.number_of_copies 1 1 1 'DIMER' 2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__em_entity_assembly_list.id _item_description.description ; The value of _em_entity_assembly_list.id must uniquely identify the component. ; _item.name '_em_entity_assembly_list.id' _item.category_id em_entity_assembly_list _item.mandatory_code yes _item_type.code code save_ save__em_entity_assembly_list.entity_id _item_description.description ; A pointer to entity id. ; _item.name '_em_entity_assembly_list.entity_id' _item.category_id em_entity_assembly_list _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_entity_assembly_list.entity_id' _item_linked.parent_name '_entity.id' save_ save__em_entity_assembly_list.entity_assembly_id _item_description.description ; This data item is a pointer to _em_entity_assembly.id in the ENTITY_ASSEMBLY category. ; _item.name '_em_entity_assembly_list.entity_assembly_id' _item.category_id em_entity_assembly_list _item.mandatory_code yes _item_type.code code save_ save__em_entity_assembly_list.oligomeric_details _item_description.description ; The oligomeric state of the entity. ; _item.name '_em_entity_assembly_list.oligomeric_details' _item.category_id em_entity_assembly_list _item.mandatory_code no _item_type.code line save_ save__em_entity_assembly_list.number_of_copies _item_description.description ; The number of copies of the entity. ; _item.name '_em_entity_assembly_list.number_of_copies' _item.category_id em_entity_assembly_list _item.mandatory_code no _item_type.code int save_ ##################### ## EM_VIRUS_ENTITY ## ##################### save_em_virus_entity _category.description ; Data items in the EM_VIRUS_ENTITY category record details of the icosahedral virus. ; _category.id em_virus_entity _category.mandatory_code no loop_ _category_key.name '_em_virus_entity.id' '_em_virus_entity.entity_assembly_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; loop_ _em_virus_entity.id _em_virus_entity.virus_host_category _em_virus_entity.virus_host_species _em_virus_entity.virus_type _em_virus_entity.virus_isolate _em_virus_entity.ictvdb_id _em_virus_entity.entity_assembly_id _em_virus_entity.enveloped _em_virus_entity.empty 1 'VERTERBRATES' 'HOMO SAPIENS' 'VIRUS' 'STRAIN' '00.073.0.01.023' 1 'YES' 'NO' ; save_ save__em_virus_entity.id _item_description.description ; Is the unique identifier for VIRUS_ENTITY category. ; _item.name '_em_virus_entity.id' _item.category_id em_virus_entity _item.mandatory_code yes _item_type.code code save_ save__em_virus_entity.virus_host_category _item_description.description ; The host category description for the virus. ; _item.name '_em_virus_entity.virus_host_category' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code line loop_ _item_examples.case ALGAE ARCHAEA 'BACTERIA(EUBACTERIA)' FUNGI INVERTEBRATES 'PLANTAE (HIGHER PLANTS)' PROTOZOA VERTEBRATES save_ save__em_virus_entity.virus_host_species _item_description.description ; The host species from which the virus was isolated. ; _item.name '_em_virus_entity.virus_host_species' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'homo sapiens' 'gallus gallus' save_ save__em_virus_entity.virus_host_growth_cell _item_description.description ; The host cell from which the virus was isolated. ; _item.name '_em_virus_entity.virus_host_growth_cell' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'HELA' 'CHO' save_ save__em_virus_entity.virus_type _item_description.description ; The type of virus. ; _item.name '_em_virus_entity.virus_type' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code line loop_ _item_examples.case VIRION SATELLITE PRION VIROID 'VIRUS-LIKE PARTICLE' save_ save__em_virus_entity.virus_isolate _item_description.description ; The isolate from which the virus was obtained. ; _item.name '_em_virus_entity.virus_isolate' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value STRAIN SEROTYPE SEROCOMPLEX SUBSPECIES SPECIES save_ save__em_virus_entity.ictvdb_id _item_description.description ; The International Committee on Taxonomy of Viruses (ICTV) Taxon Identifier is the Virus Code used throughout the ICTV database (ICTVdb). The ICTVdb id is the appropriate identifier used by the International Committee on Taxonomy of Viruses Resource. Reference: Virus Taxonomy, Academic Press (1999). ISBN:0123702003. ; _item.name '_em_virus_entity.ictvdb_id' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code line loop_ _item_examples.case '01.0.2.0.001' '01.0.2.0.002' save_ save__em_virus_entity.entity_assembly_id _item_description.description ; This data item is a pointer to _em_virus_entity.id in the ENTITY_ASSEMBLY category. ; _item.name '_em_virus_entity.entity_assembly_id' _item.category_id em_virus_entity _item.mandatory_code yes _item_type.code code save_ save__em_virus_entity.enveloped _item_description.description ; Flag to indicate if the virus is enveloped or not. ; _item.name '_em_virus_entity.enveloped' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value YES NO save_ save__em_virus_entity.empty _item_description.description ; Flag to indicate if the virus is empty or not. ; _item.name '_em_virus_entity.empty' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value YES NO save_ save__em_virus_entity.details _item_description.description ; Additional details about this virus entity ; _item.name '_em_virus_entity.details' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code text save_ ########################## ## EM_ICOS_VIRUS_SHELLS ## ########################## save_em_icos_virus_shells _category.description ; Data items in the EM_ICOS_VIRUS_SHELLS category record details of the viral shell number, diameter of each shell and triangulation number. ; _category.id em_icos_virus_shells _category.mandatory_code no loop_ _category_key.name '_em_icos_virus_shells.virus_entity_id' '_em_icos_virus_shells.id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; loop_ _em_icos_virus_shells.virus_entity_id _em_icos_virus_shells.id _em_icos_virus_shells.shell_diameter _em_icos_virus_shells.triangulation_num 1 1 400 4 ; save_ save__em_icos_virus_shells.virus_entity_id _item_description.description ; The value of _em_icos_virus_shells.virus_entity_id is a pointer to _em_virus_entity.id in the VIRUS_ENTITY category. ; _item.name '_em_icos_virus_shells.virus_entity_id' _item.category_id em_icos_virus_shells _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_icos_virus_shells.virus_entity_id' _item_linked.parent_name '_em_virus_entity.id' save_ save__em_icos_virus_shells.id _item_description.description ; The value of _em_em_icos_virus_shells.id must uniquely identify the number and diameter of each virus protein shell and its triangulation number. ; _item.name '_em_icos_virus_shells.id' _item.category_id em_icos_virus_shells _item.mandatory_code yes _item_type.code code save_ save__em_icos_virus_shells.shell_diameter _item_description.description ; The value of the diameter (in angstroms) for each protein shell of the virus. ; _item.name '_em_icos_virus_shells.shell_diameter' _item.category_id em_icos_virus_shells _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__em_icos_virus_shells.triangulation_num _item_description.description ; The triangulation number (T number) is a geometric and abstract concept that does not correspond to the structural components of an individul virus. It refers to the organisation of the geometric figure. The triangulation number, T is given by the following relationship: T= h*2 + hk +k*2, where h and k are positive integers which define the position of the five-fold vertex on the original hexagonal net. ; _item.name '_em_icos_virus_shells.triangulation_num' _item.category_id em_icos_virus_shells _item.mandatory_code no _item_type.code int _item_examples.case 4 save_ ########################### ## EM_SAMPLE_PREPARATION ## ########################### save_em_sample_preparation _category.description ; Data items in the EM_SAMPLE_PREPARATION category record details of sample conditions prior to loading onto grid support. ; _category.id em_sample_preparation _category.mandatory_code no loop_ _category_key.name '_em_sample_preparation.id' '_em_sample_preparation.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_sample_preparation.entry_id 1DYL _em_sample_preparation.id 1 _em_sample_preparation.ph 7.6 _em_sample_preparation.buffer_id 1 _em_sample_preparation.sample_concentration 5 _em_sample_preparation.2d_crystal_grow_id . _em_sample_preparation.support.id 1 ; save_ save__em_sample_preparation.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_sample_preparation.entry_id' _item.category_id em_sample_preparation _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_sample_preparation.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_sample_preparation.id _item_description.description ; The value of _em_sample_preparation.id must uniquely identify the sample preparation. ; _item.name '_em_sample_preparation.id' _item.category_id em_sample_preparation _item.mandatory_code yes _item_type.code code save_ save__em_sample_preparation.ph _item_description.description ; The pH value of the observed sample buffer. ; _item.name '_em_sample_preparation.ph' _item.category_id em_sample_preparation _item.mandatory_code no _item_type.code float save_ save__em_sample_preparation.buffer_id _item_description.description ; This data item is a pointer to _em_buffer.id in the BUFFER category. ; _item.name '_em_sample_preparation.buffer_id' _item.category_id em_sample_preparation _item.mandatory_code no _item_type.code code save_ save__em_sample_preparation.sample_concentration _item_description.description ; The value of the concentration (mg/mL for mg per milliliter) of the complex in the sample. ; _item.name '_em_sample_preparation.sample_concentration' _item.category_id em_sample_preparation _item.mandatory_code no _item_type.code float _item_units.code mg_per_ml save_ save__em_sample_preparation.2d_crystal_grow_id _item_description.description ; This data item is a pointer to _em_2d_crystal_grow.id in the 2D_CRYSTAL_GROW category. ; _item.name '_em_sample_preparation.2d_crystal_grow_id' _item.category_id em_sample_preparation _item.mandatory_code no _item_type.code code save_ save__em_sample_preparation.support_id _item_description.description ; This data item is a pointer to _em_sample_support.id in the EM_SAMPLE_SUPPORT category. ; _item.name '_em_sample_preparation.support_id' _item.category_id em_sample_preparation _item.mandatory_code no _item_type.code code save_ ####################### ## EM_SAMPLE_SUPPORT ## ####################### save_em_sample_support _category.description ; Data items in the EM_SAMPLE_SUPPORT category record details of the electron microscope grid type, grid support film and pretreatment of whole before sample is applied ; _category.id em_sample_support _category.mandatory_code no _category_key.name '_em_sample_support.id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_sample_support.id 1 _em_sample_support.film_material 'HOLEY CARBON' _em_sample_support.method . _em_sample_support.grid_material COPPER _em_sample_support.grid_mesh_size 400 _em_sample_support.grid_type MESH _em_sample_support.pretreatment 'GLOW DISCHARGE' _em_sample_support.details . _em_sample_support.citation_id 2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__em_sample_support.id _item_description.description ; The value of _em_sample_support.id must uniquely identify the sample support. ; _item.name '_em_sample_support.id' _item.category_id em_sample_support _item.mandatory_code yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_em_imaging.sample_support_id' '_em_sample_support.id' '_em_sample_preparation.support_id' '_em_sample_support.id' save_ save__em_sample_support.film_material _item_description.description ; The support material covering the em grid. ; _item.name '_em_sample_support.film_material' _item.category_id em_sample_support _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value CARBON 'FORMVAR PLUS CARBON' 'CELLULOSE ACETATE PLUS CARBON' 'PARLODION PLUS CARBON' 'HOLEY CARBON' save_ save__em_sample_support.method _item_description.description ; A description of the method used to produce the support film. ; _item.name '_em_sample_support.method' _item.category_id em_sample_support _item.mandatory_code no _item_type.code text _item_examples.case '1%formvar in chloroform cast on distilled water' save_ save__em_sample_support.grid_material _item_description.description ; The name of the material from which the grid is made. ; _item.name '_em_sample_support.grid_material' _item.category_id em_sample_support _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value COPPER COPPER/PALLADIUM COPPER/RHODIUM GOLD NICKEL PLATINUM TUNGSTEN TITANIUM MOLYBDENUM save_ save__em_sample_support.grid_mesh_size _item_description.description ; The value of the mesh size (per inch) of the em grid. ; _item.name '_em_sample_support.grid_mesh_size' _item.category_id em_sample_support _item.mandatory_code no _item_type.code int _item_examples.case 400 save_ save__em_sample_support.grid_type _item_description.description ; A description of the grid type. ; _item.name '_em_sample_support.grid_type' _item.category_id em_sample_support _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value SLOT APERTURE DIAMOND HEXAGONAL save_ save__em_sample_support.pretreatment _item_description.description ; A description of the grid plus support film pretreatment. ; _item.name '_em_sample_support.pretreatment' _item.category_id em_sample_support _item.mandatory_code no _item_type.code text _item_examples.case 'glow-discharged for 30 sec in argon' save_ save__em_sample_support.details _item_description.description ; A description of any additional details concerning the sample support. ; _item.name '_em_sample_support.details' _item.category_id em_sample_support _item.mandatory_code no _item_type.code text _item_examples.case 'This grid plus sample was kept at -170 deg C for a month before use' save_ save__em_sample_support.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_sample_support.citation_id' _item.category_id em_sample_support _item.mandatory_code no _item_linked.child_name '_em_sample_support.citation_id' _item_linked.parent_name '_citation.id' _item_type.code code save_ ########################## ## EM_2D_CRYSTAL_GROW ## ########################## save_em_2d_crystal_grow _category.description ; Data items in the EM_2D_CRYSTAL_GROW category record details of growth conditions for 2d crystal samples. ; _category.id em_2d_crystal_grow _category.mandatory_code no _category_key.name '_em_2d_crystal_grow.id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1AT9 and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_2d_crystal_grow.id 1 _em_2d_crystal_grow.method . _em_2d_crystal_grow.apparatus . _em_2d_crystal_grow.atmosphere 'room air' _em_2d_crystal_grow.pH 5.2 _em_2d_crystal_grow.temp 18 _em_2d_crystal_grow.time . _em_2d_crystal_grow.buffer_id 2 _em_2d_crystal_grow.details 'on grid' _em_2d_crystal_grow.number_2d_crystals 129 _em_2d_crystal_grow.mean_2d_crystal_size . _em_2d_crystal_grow.citation_id 2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__em_2d_crystal_grow.id _item_description.description ; The value of _em_2d_crystal_grow.crystal_id must uniquely identify the sample 2d crystal. ; _item.name '_em_2d_crystal_grow.id' _item.category_id em_2d_crystal_grow _item.mandatory_code yes _item_type.code code save_ save__em_2d_crystal_grow.method _item_description.description ; The method used for growing the crystals. ; _item.name '_em_2d_crystal_grow.method' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code line _item_examples.case 'lipid monolayer' save_ save__em_2d_crystal_grow.apparatus _item_description.description ; The type of the apparatus used for growing the crystals. ; _item.name '_em_2d_crystal_grow.apparatus' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code line _item_examples.case 'Langmuir trough' save_ save__em_2d_crystal_grow.atmosphere _item_description.description ; The type of atmosphere in which crystals were grown. ; _item.name '_em_2d_crystal_grow.atmosphere' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code line _item_examples.case 'room air' save_ save__em_2d_crystal_grow.pH _item_description.description ; the pH value used for growing the crystals. ; _item.name '_em_2d_crystal_grow.pH' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code float _item_examples.case 4.7 save_ save__em_2d_crystal_grow.temp _item_description.description ; The value of the temperature in degrees Kelvin used for growing the crystals. ; _item.name '_em_2d_crystal_grow.temp' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code float _item_units.code kelvins _item_examples.case 293 save_ save__em_2d_crystal_grow.time _item_description.description ; The length of time required to grow the crystals. ; _item.name '_em_2d_crystal_grow.time' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code line _item_examples.case 'approximately 2 days' save_ save__em_2d_crystal_grow.buffer_id _item_description.description ; This data item is a pointer to _em_buffer.id in the BUFFER category. ; _item.name '_em_2d_crystal_grow.buffer_id' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code code save_ save__em_2d_crystal_grow.details _item_description.description ; Any additional items concerning 2d crystal growth. ; _item.name '_em_2d_crystal_grow.details' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code text save_ save__em_2d_crystal_grow.number_2d_crystals _item_description.description ; The number of 2d crystals imaged. ; _item.name '_em_2d_crystal_grow.number_2d_crystals' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code int save_ save__em_2d_crystal_grow.mean_2d_crystal_size _item_description.description ; The approximate size (microns squared) of 2d crystals imaged. ; _item.name '_em_2d_crystal_grow.mean_2d_crystal_size' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code float _item_units.code microns_squared save_ save__em_2d_crystal_grow.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_2d_crystal_grow.citation_id' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_linked.child_name '_em_2d_crystal_grow.citation_id' _item_linked.parent_name '_citation.id' _item_type.code code save_ ############### ## EM_BUFFER ## ############### save_em_buffer _category.description ; Data items in the BUFFER category record details of the sample buffer. ; _category.id em_buffer _category.mandatory_code no _category_key.name '_em_buffer.id' loop_ _category_group.id 'inclusive_group' 'em_group' save_ save__em_buffer.id _item_description.description ; The value of _em_buffer.id must uniquely identify the sample buffer. ; _item.name '_em_buffer.id' _item.category_id em_buffer _item.mandatory_code yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_em_2d_crystal_grow.buffer_id' '_em_buffer.id' '_em_sample_preparation.buffer_id' '_em_buffer.id' '_em_buffer_components.buffer_id' '_em_buffer.id' save_ save__em_buffer.name _item_description.description ; The name of the buffer. ; _item.name '_em_buffer.name' _item.category_id em_buffer _item.mandatory_code no _item_type.code line _item_examples.case 'Acetic acid' save_ save__em_buffer.details _item_description.description ; Any additional details to do with buffer. ; _item.name '_em_buffer.details' _item.category_id em_buffer _item.mandatory_code no _item_type.code text _item_examples.case 'aerated' save_ ########################## ## EM_BUFFER_COMPONENTS ## ########################## save_em_buffer_components _category.description ; Constituents of buffer in sample ; _category.id em_buffer_components _category.mandatory_code no loop_ _category_key.name '_em_buffer_components.buffer_id' '_em_buffer_components.id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ;loop_ _em_buffer_components.buffer_id _em_buffer_components.id _em_buffer_components.name _em_buffer_components.volume _em_buffer_components.conc _em_buffer_components.details 1 1 'NaCl' '0.200 ' '4 ' . 1 2 'Acetic Acid' '0.047 ' '100' . 1 3 'water' '0.700 ' 'neat' . ; save_ save__em_buffer_components.id _item_description.description ; The value of _em_buffer_components.id must uniquely identify a component of the buffer. ; _item.name '_em_buffer_components.id' _item.category_id em_buffer_components _item.mandatory_code yes _item_type.code code save_ save__em_buffer_components.buffer_id _item_description.description ; This data item is a pointer to _em_buffer.id in the BUFFER category. ; _item.name '_em_buffer_components.buffer_id' _item.category_id em_buffer_components _item.mandatory_code yes _item_type.code code save_ save__em_buffer_components.name _item_description.description ; The name of each buffer component. ; _item.name '_em_buffer_components.name' _item.category_id em_buffer_components _item.mandatory_code no _item_type.code line _item_examples.case 'Acetic acid' save_ save__em_buffer_components.volume _item_description.description ; The volume of buffer component. ; _item.name '_em_buffer_components.volume' _item.category_id em_buffer_components _item.mandatory_code no _item_type.code code _item_examples.case 0.200 save_ save__em_buffer_components.conc _item_description.description ; The millimolar concentration of buffer component. ; _item.name '_em_buffer_components.conc' _item.category_id em_buffer_components _item.mandatory_code no _item_type.code code _item_examples.case 200 save_ save__em_buffer_components.details _item_description.description ; Any additional details to do with buffer composition. ; _item.name '_em_buffer_components.details' _item.category_id em_buffer_components _item.mandatory_code no _item_type.code text _item_examples.case 'pH adjusted with NaOH' save_ ###################### ## EM_VITRIFICATION ## ###################### save_em_vitrification _category.description ; Data items in the EM_VITRIFICATION category record details about the method and cryogen used in rapid freezing of the sample on the grid prior to its insertion in the electron microscope ; _category.id em_vitrification _category.mandatory_code no loop_ _category_key.name '_em_vitrification.id' '_em_vitrification.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_vitrification.entry_id 1DYL _em_vitrification.id 1 _em_vitrification.sample_preparation_id 1 _em_vitrification.cryogen_name "ETHANE" _em_vitrification.humidity 90 _em_vitrification.temp 95 _em_vitrification.instrument . _em_vitrification.method "PLUNGE VITRIFICATION" _em_vitrification.time_resolved_state . _em_vitrification.citation_id 1 _em_vitrification.details ; SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626-0300 CRYOTRANSFER HOLDER. ; ; save_ save__em_vitrification.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_vitrification.entry_id' _item.category_id em_vitrification _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_vitrification.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_vitrification.id _item_description.description ; The value of _em_vitrification.id must uniquely identify the vitrification procedure. ; _item.name '_em_vitrification.id' _item.category_id em_vitrification _item.mandatory_code yes _item_type.code code save_ save__em_vitrification.sample_preparation_id _item_description.description ; This data item is a pointer to _em_sample_preparation.id in the EM_SAMPLE_PREPARATION category. ; _item.name '_em_vitrification.sample_preparation_id' _item.category_id em_vitrification _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_vitrification.sample_preparation_id' _item_linked.parent_name '_em_sample_preparation.id' save_ save__em_vitrification.cryogen_name _item_description.description ; This is the name of the cryogen. ; _item.name '_em_vitrification.cryogen_name' _item.category_id em_vitrification _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value HELIUM NITROGEN PROPANE ETHANE METHANE 'FREON 22' 'FREON 12' save_ save__em_vitrification.humidity _item_description.description ; The humidity (%) in the vicinity of the vitrification process. ; _item.name '_em_vitrification.humidity' _item.category_id em_vitrification _item.mandatory_code no _item_type.code line _item_examples.case 90 save_ save__em_vitrification.temp _item_description.description ; The temperature (in degrees Kelvin) at which vitrification took place. ; _item.name '_em_vitrification.temp' _item.category_id em_vitrification _item.mandatory_code no _item_type.code float _item_units.code kelvins _item_examples.case 4.2 save_ save__em_vitrification.instrument _item_description.description ; The type of instrument used in the vitrification process. ; _item.name '_em_vitrification.instrument' _item.category_id em_vitrification _item.mandatory_code no _item_type.code line _item_examples.case 'Reichert plunger' save_ save__em_vitrification.method _item_description.description ; The procedure for vitrification. ; _item.name '_em_vitrification.method' _item.category_id em_vitrification _item.mandatory_code no _item_type.code text _item_examples.case 'blot for 2 seconds before plunging' save_ save__em_vitrification.time_resolved_state _item_description.description ; The length of time after an event effecting the sample that vitrification was induced and a description of the event. ; _item.name '_em_vitrification.time_resolved_state' _item.category_id em_vitrification _item.mandatory_code no _item_type.code text _item_examples.case '30 msec after spraying with effector'' save_ save__em_vitrification.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_vitrification.citation_id' _item.category_id em_vitrification _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_vitrification.citation_id' _item_linked.parent_name '_citation.id' save_ save__em_vitrification.details _item_description.description ; Any additional details relating to vitrification. ; _item.name '_em_vitrification.details' _item.category_id em_vitrification _item.mandatory_code no _item_type.code text _item_examples.case 'argon atmosphere' save_ ################ ## EM_IMAGING ## ################ save_em_imaging _category.description ; Data items in the EM_IMAGING category record details about the parameters used in imaging the sample in the electron microscope. ; _category.id em_imaging _category.mandatory_code no loop_ _category_key.name '_em_imaging.entry_id' '_em_imaging.id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_imaging.entry_id 1DYL _em_imaging.id 1 _em_imaging.sample_support_id 1 _em_imaging.microscope_model 'FEI/PHILIPS CM200 FEG' _em_imaging.specimen_holder_type 'cryotransfer' _em_imaging.specimen_holder_model 'gatan 626-0300' _em_imaging.details . _em_imaging.date 1998-15-06 _em_imaging.accelerating_voltage 200 _em_imaging.illumination_mode 'bright field' _em_imaging.mode 'low dose' _em_imaging.nominal_cs 2.0 _em_imaging.nominal_defocus_min 975 _em_imaging.nominal_defocus_max 7600 _em_imaging.tilt_angle_min 0 _em_imaging.tilt_angle_max 0 _em_imaging.nominal_magnification 50000 _em_imaging.calibrated_magnification . _em_imaging.electron_source 'FEG' _em_imaging.electron_dose . _em_imaging.energy_filter . _em_imaging.energy_window . _em_imaging.citation_id 1 _em_imaging.temperature 95 _em_imaging.detector_distance . _em_imaging.recording_temp_range . ; save_ save__em_imaging.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_imaging.entry_id' _item.category_id em_imaging _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_imaging.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_imaging.id _item_description.description ; The value of _em_imaging.id must uniquely identify each imaging experiment. ; _item.name '_em_imaging.id' _item.category_id em_imaging _item.mandatory_code yes _item_type.code code save_ save__em_imaging.sample_support_id _item_description.description ; This data item is a pointer to _em_sample_support.id in the EM_SAMPLE_SUPPORT category. ; _item.name '_em_imaging.sample_support_id' _item.category_id em_imaging _item.mandatory_code yes _item_type.code code save_ save__em_imaging.detector_id _item_description.description ; The value of _em_imaging.detector_id must uniquely identify the type of detector used in the experiment. ; _item.name '_em_imaging.detector_id' _item.category_id em_imaging _item.mandatory_code yes _item_type.code code save_ save__em_imaging.scans_id _item_description.description ; The value of _em_imaging.scans_id must uniquely identify the image_scans used in the experiment. ; _item.name '_em_imaging.scans_id' _item.category_id em_imaging _item.mandatory_code yes _item_type.code code save_ save__em_imaging.microscope_model _item_description.description ; The name of the model of microscope. ; _item.name '_em_imaging.microscope_model' _item.category_id em_imaging _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'HITACHI H8100' 'HITACHI HF2000' 'HITACHI HF2000-UHR' 'HITACHI H9000-UHR' 'HITACHI H9000-NAR' 'HITACHI 300KEV FEG' 'HITACHI HU1250' 'HITACHI H-1500' 'JEOL 2000EX' 'JEOL 2010HT' 'JEOL 2010UHR' 'JEOL 2010F' 'JEOL 3010HT' 'JEOL 3010UHR' 'JEOL KYOTO-3000SFF' 'JEOL 4000EX' 'JEOL HAREM' 'JEOL ARM-1000' 'JEOL KYOTO-1000' 'JEOL ARM-1250' 'FEI/PHILIPS CM120T' 'FEI/PHILIPS CM200T' 'FEI/PHILIPS CM20/ST' 'FEI/PHILIPS CM20/SOPHIE' 'FEI/PHILIPS CM200FEG/ST' 'FEI/PHILIPS CM20/UT' 'FEI/PHILIPS CM200FEG/UT' 'FEI/PHILIPS CM30/T' 'FEI/PHILIPS CM300FEG/T' 'FEI/PHILIPS CM300FEG/HE' 'FEI/PHILIPS CM30/ST' 'FEI/PHILIPS CM300FEG/ST' 'FEI/PHILIPS CM300FEG/UT' 'FEI TECNAI 12' 'FEI TECNAI 20' 'FEI TECNAI F20' 'FEI TECNAI F30' 'FEI MORGAGNI' save_ save__em_imaging.specimen_holder_type _item_description.description ; The type of specimen holder used during imaging. ; _item.name '_em_imaging.specimen_holder_type' _item.category_id em_imaging _item.mandatory_code no _item_type.code line _item_examples.case 'cryo' save_ save__em_imaging.specimen_holder_model _item_description.description ; The name of the model of specimen holder used during imaging. ; _item.name '_em_imaging.specimen_holder_model' _item.category_id em_imaging _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value 'GATAN HELIUM' 'GATAN LIQUID NITROGEN' OTHER save_ save__em_imaging.details _item_description.description ; Any additional imaging details. ; _item.name '_em_imaging.details' _item.category_id em_imaging _item.mandatory_code no _item_type.code text _item_examples.case 'weak beam illumination' save_ save__em_imaging.date _item_description.description ; Date (YYYY-MM-DD) of imaging experiment or the date at which a series of experiments began. ; _item.name '_em_imaging.date' _item.category_id em_imaging _item.mandatory_code no # _item_type.code yyyy-mm-dd _item_type.code line _item_examples.case '2001-05-08' save_ save__em_imaging.accelerating_voltage _item_description.description ; A value of accelerating voltage (in kV) used for imaging. ; _item.name '_em_imaging.accelerating_voltage' _item.category_id em_imaging _item.mandatory_code no _item_type.code int _item_units.code kilovolts _item_examples.case 300 save_ save__em_imaging.illumination_mode _item_description.description ; The mode of illumination. ; _item.name '_em_imaging.illumination_mode' _item.category_id em_imaging _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'FLOOD BEAM' 'FLOOD BEAM LOW DOSE' 'SPOT SCAN' OTHER save_ save__em_imaging.mode _item_description.description ; The mode of imaging. ; _item.name '_em_imaging.mode' _item.category_id em_imaging _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'BRIGHT FIELD' 'DARK FIELD' DIFFRACTION OTHER save_ save__em_imaging.nominal_cs _item_description.description ; The spherical aberration coefficient (Cs) in millimetres, of the objective lens. ; _item.name '_em_imaging.nominal_cs' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code millimetres _item_examples.case 1.4 save_ save__em_imaging.nominal_defocus_min _item_description.description ; The minimum defocus value of the objective lens (in nanometres) used to obtain the recorded images. ; _item.name '_em_imaging.nominal_defocus_min' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code nanometres _item_examples.case 975 save_ save__em_imaging.nominal_defocus_max _item_description.description ; The maximum defocus value of the objective lens (in nanometres) used to obtain the recorded images. ; _item.name '_em_imaging.nominal_defocus_max' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code nanometres _item_examples.case 7600 save_ save__em_imaging.tilt_angle_min _item_description.description ; The minimum angle at which the specimen was tilted to obtain recorded images. ; _item.name '_em_imaging.tilt_angle_min' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code degrees _item_examples.case 0 save_ save__em_imaging.tilt_angle_max _item_description.description ; The maximum angle at which the specimen was tilted to obtain recorded images. ; _item.name '_em_imaging.tilt_angle_max' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code degrees _item_examples.case 60 save_ save__em_imaging.nominal_magnification _item_description.description ; The magnification indicated by the microscope readout. ; _item.name '_em_imaging.nominal_magnification' _item.category_id em_imaging _item.mandatory_code no _item_type.code int _item_examples.case 60000 save_ save__em_imaging.calibrated_magnification _item_description.description ; The magnification value obtained for a known standard just prior to, during or just after the imaging experiment. ; _item.name '_em_imaging.calibrated_magnification' _item.category_id em_imaging _item.mandatory_code no _item_type.code int _item_examples.case 61200 save_ save__em_imaging.electron_source _item_description.description ; The source of electrons. The electron gun. ; _item.name '_em_imaging.electron_source' _item.category_id em_imaging _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'FIELD EMISSION GUN' LAB6 'TUNGSTEN HAIRPIN' 'SCHOTTKY FIELD EMISSION GUN' OTHER save_ save__em_imaging.electron_dose _item_description.description ; The electron dose received by the specimen (electrons per square angstrom). ; _item.name '_em_imaging.electron_dose' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code electrons_angstrom_squared _item_examples.case 0.9 save_ save__em_imaging.energy_filter _item_description.description ; The type of energy filter spectrometer apparatus. ; _item.name '_em_imaging.energy_filter' _item.category_id em_imaging _item.mandatory_code no _item_type.code line _item_examples.case 'FEI' save_ save__em_imaging.energy_window _item_description.description ; The energy filter range in electron volts (eV)set by spectrometer. ; _item.name '_em_imaging.energy_window' _item.category_id em_imaging _item.mandatory_code no _item_type.code line _item_units.code electron_volts _item_examples.case '0 - 15' save_ save__em_imaging.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_imaging.citation_id' _item.category_id em_imaging _item.mandatory_code no _item_linked.child_name '_em_imaging.citation_id' _item_linked.parent_name '_citation.id' _item_type.code code save_ save__em_imaging.temperature _item_description.description ; The mean specimen stage temperature (degrees Kelvin) during imaging in the microscope. ; _item.name '_em_imaging.temperature' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code kelvins save_ save__em_imaging.detector_distance _item_description.description ; The camera length (in millimetres). The camera length is the product of the objective focal length and the combined magnification of the intermediate and projector lenses when the microscope is operated in the diffraction mode. ; _item.name '_em_imaging.detector_distance' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code millimetres save_ save__em_imaging.recording_temperature_minimum _item_description.description ; The specimen temperature minimum (degrees Kelvin) for the duration of imaging. ; _item.name '_em_imaging.recording_temperature_minimum' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code kelvins save_ save__em_imaging.recording_temperature_maximum _item_description.description ; The specimen temperature maximum (degrees Kelvin) for the duration of imaging. ; _item.name '_em_imaging.recording_temperature_maximum' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code kelvins save_ ################# ## EM_DETECTOR ## ################# save_em_detector _category.description ; Data items in the EM_DETECTOR category record details of the image detector type. ; _category.id em_detector _category.mandatory_code no loop_ _category_key.name '_em_detector.entry_id' '_em_detector.id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_detector.entry_id 1DYL _em_detector.id 1 _em_detector.details . _em_detector.type 'KODAK SO163 FILM' _em_detector.detective_quantum_efficiency . ; save_ save__em_detector.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_detector.entry_id' _item.category_id em_detector _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_detector.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_detector.id _item_description.description ; The value of _em_detector.id must uniquely identify the detector used for imaging. ; _item.name '_em_detector.id' _item.category_id em_detector _item.mandatory_code yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_em_imaging.detector_id' '_em_detector.id' save_ save__em_detector.details _item_description.description ; Any additional information about the detection system. ; _item.name '_em_detector.details' _item.category_id em_detector _item.mandatory_code no _item_type.code text save_ save__em_detector.type _item_description.description ; The detector type used for recording images. Usually film or CCD camera. ; _item.name '_em_detector.type' _item.category_id em_detector _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'KODAK SO163 FILM' 'GATAN 673' 'GATAN 676' 'GATAN 692' 'GATAN 794' 'GATAN 1000' 'GATAN 4000' 'TVIPS BIOCAM' 'TVIPS TEMCAM F214' 'TVIPS TEMCAM F224' 'TVIPS FASTSCAN F114' PROSCAN AMT save_ save__em_detector.detective_quantum_efficiency _item_description.description ; The detective_quantum_efficiency (DQE)is defined as the square of the signal-to-noise ratio in the recording device divided by the square of the signal-to-ratio in the electron beam: (SIGNAL/NOISE)2 recording device DQE = ------------------------------- (SIGNAL/NOISE)2 electron beam A DQE value of 1 indicates a perfect recorder. "DQE = 0.25" menas that the signal-to-noise ratio is reduced by half in the recording step. (0.5)**2 DQE = --------- = 0.25. (1.0)**2 ; _item.name '_em_detector.detective_quantum_efficiency' _item.category_id em_detector _item.mandatory_code no _item_type.code float _item_examples.case 0.25 save_ #################### ## EM_IMAGE_SCANS ## #################### save_em_image_scans _category.description ; Data items in the EM_IMAGE_SCANS category record details of the image scanning device (microdensitometer) and parameters for digitization of the image. ; _category.id em_image_scans _category.mandatory_code no loop_ _category_key.name '_em_image_scans.entry_id' '_em_image_scans.id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_image_scans.entry_id 1DYL _em_image_scans.id 2 _em_image_scans.number_digital_images 48 _em_image_scans.details . _em_image_scans.scanner_model . _em_image_scans.sampling_size . _em_image_scans.od_range . _em_image_scans.quant_bit_number . _em_image_scans.citation_id 1 ; save_ save__em_image_scans.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_image_scans.entry_id' _item.category_id em_image_scans _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_image_scans.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_image_scans.id _item_description.description ; The value of _em_image_scans.id must uniquely identify the images scanned. ; _item.name '_em_image_scans.id' _item.category_id em_image_scans _item.mandatory_code yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_em_imaging.scans_id' '_em_image_scans.id' save_ save__em_image_scans.number_digital_images _item_description.description ; The number of images scanned and digitised. ; _item.name '_em_image_scans.number_digital_images' _item.category_id em_image_scans _item.mandatory_code no _item_type.code int save_ save__em_image_scans.details _item_description.description ; Any additional details about scanning images. ; _item.name '_em_image_scans.details' _item.category_id em_image_scans _item.mandatory_code no _item_type.code text save_ save__em_image_scans.scanner_model _item_description.description ; The scanner model. ; _item.name '_em_image_scans.scanner_model' _item.category_id em_image_scans _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value 'ZEISS SCAI' 'EMIL 10' OPTRONICS 'PERKIN ELMER' TEMSCAN OTHER save_ save__em_image_scans.sampling_size _item_description.description ; The sampling step size (microns) set on the scanner. ; _item.name '_em_image_scans.sampling_size' _item.category_id em_image_scans _item.mandatory_code no _item_type.code float _item_units.code microns save_ save__em_image_scans.od_range _item_description.description ; The optical density range (OD=-log 10 transmission). To the eye OD=1 appears light grey and OD=3 is opaque. ; _item.name '_em_image_scans.od_range' _item.category_id em_image_scans _item.mandatory_code no _item_type.code float _item_examples.case 1.4 save_ save__em_image_scans.quant_bit_size _item_description.description ; The number of bits per pixel. ; _item.name '_em_image_scans.quant_bit_size' _item.category_id em_image_scans _item.mandatory_code no _item_type.code int _item_examples.case 8 save_ save__em_image_scans.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_image_scans.citation_id' _item.category_id em_image_scans _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_image_scans.citation_id' _item_linked.parent_name '_citation.id' save_ ################################ ## EM_2D_PROJECTION_SELECTION ## ################################ save_em_2d_projection_selection _category.description ; Data items in the EM_2D_PROJECTION_SELECTION category record details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs. ; _category.id em_2d_projection_selection _category.mandatory_code no _category_key.name '_em_2d_projection_selection.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_2d_projection_selection.entry_id 1 _em_2d_projection_selection.number_particles 5267 _em_2d_projection_selection.software_name 1 _em_2d_projection_selection.method 'INTERACTIVE' _em_2d_projection_selection.details . _em_2d_projection_selection.citation_id 1 ; save_ save__em_2d_projection_selection.entry_id _item_description.description ; The value of _em_2d_projection_selection.entry_id points to the ENTRY category. ; _item.name '_em_2d_projection_selection.entry_id' _item.category_id em_2d_projection_selection _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_2d_projection_selection.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_2d_projection_selection.num_particles _item_description.description ; The number of particles selected from the projection set of images. ; _item.name '_em_2d_projection_selection.num_particles' _item.category_id em_2d_projection_selection _item.mandatory_code no _item_type.code int _item_examples.case 840 save_ save__em_2d_projection_selection.software_name _item_description.description ; This data item is a pointer to _software.name in the SOFTWARE category. ; _item.name '_em_2d_projection_selection.software_name' _item.category_id em_2d_projection_selection _item.mandatory_code no _item_type.code line # _item_linked.child_name '_em_2d_projection_selection.software_name' # _item_linked.parent_name '_software.name' save_ save__em_2d_projection_selection.method _item_description.description ; The method used for selecting observed assemblies. ; _item.name '_em_2d_projection_selection.method' _item.category_id em_2d_projection_selection _item.mandatory_code no _item_type.code text _item_examples.case 'particles picked interactively from monitor' save_ save__em_2d_projection_selection.details _item_description.description ; Any additional details used for selecting observed assemblies. ; _item.name '_em_2d_projection_selection.details' _item.category_id em_2d_projection_selection _item.mandatory_code no _item_type.code text _item_examples.case 'negative monitor contrast facilitated particle picking' save_ save__em_2d_projection_selection.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_2d_projection_selection.citation_id' _item.category_id em_2d_projection_selection _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_2d_projection_selection.citation_id' _item_linked.parent_name '_citation.id' save_ ################################# ## EM_EULER_ANGLE_DISTRIBUTION ## ################################# save_em_euler_angle_distribution _category.description ; Data items in the EM_EULER_ANGLE_DISTRIBUTION category record details of assignment of Euler angles for projection sets of particles. ; _category.id em_euler_angle_distribution _category.mandatory_code no loop_ _category_key.name '_em_euler_angle_distribution.id' '_em_euler_angle_distribution.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_euler_angle_distribution.entry_id 1DYL _em_euler_angle_distribution.id 1 _em_euler_angle_distribution.details . _em_euler_angle_distribution.alpha . _em_euler_angle_distribution.beta . _em_euler_angle_distribution.gamma . ; save_ save__em_euler_angle_distribution.id _item_description.description ; The value of _em_euler_angle_distribution.id must uniquely identify the euler angle assignments of the projection set used in the final reconstruction. ; _item.name '_em_euler_angle_distribution.id' _item.category_id em_euler_angle_distribution _item.mandatory_code yes _item_type.code code save_ save__em_euler_angle_distribution.entry_id _item_description.description ; The value of _em_euler_angle_distribution.entry_id is a pointer to the ENTRY category. ; _item.name '_em_euler_angle_distribution.entry_id' _item.category_id em_euler_angle_distribution _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_euler_angle_distribution.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_euler_angle_distribution.details _item_description.description ; Any additional details of the euler angles distribution and assignment. ; _item.name '_em_euler_angle_distribution.details' _item.category_id em_euler_angle_distribution _item.mandatory_code no _item_type.code text save_ save__em_euler_angle_distribution.alpha _item_description.description ; The euler-alpha angle assignment. ; _item.name '_em_euler_angle_distribution.alpha' _item.category_id em_euler_angle_distribution _item.mandatory_code no _item_type.code float _item_units.code degrees _item_examples.case 90 save_ save__em_euler_angle_distribution.beta _item_description.description ; The euler-beta angle assignment. ; _item.name '_em_euler_angle_distribution.beta' _item.category_id em_euler_angle_distribution _item.mandatory_code no _item_type.code float _item_units.code degrees _item_examples.case 90 save_ save__em_euler_angle_distribution.gamma _item_description.description ; The euler-gamma angle assignment. ; _item.name '_em_euler_angle_distribution.gamma' _item.category_id em_euler_angle_distribution _item.mandatory_code no _item_type.code float _item_units.code degrees _item_examples.case 0 save_ ########################## ## EM_3D_RECONSTRUCTION ## ########################## save_em_3d_reconstruction _category.description ; Data items in the EM_3D_RECONSTRUCTION category record details of the 3D reconstruction procedure from 2D projections. ; _category.id em_3d_reconstruction _category.mandatory_code no loop_ _category_key.name '_em_3d_reconstruction.entry_id' '_em_3d_reconstruction.id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_3d_reconstruction.entry_id 1DYL _em_3d_reconstruction.id 1 _em_3d_reconstruction.method 'CROSS-COMMON LINES' _em_3d_reconstruction.citation_id 1 _em_3d_reconstruction.details . _em_3d_reconstruction.resolution 9 _em_3d_reconstruction.resolution_method . _em_3d_reconstruction.ctf_correction_method . _em_3d_reconstruction.nominal_pixel_size 2.64 _em_3d_reconstruction.actual_pixel_size 2.52 ; save_ save__em_3d_reconstruction.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_3d_reconstruction.entry_id' _item.category_id em_3d_reconstruction _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_3d_reconstruction.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_3d_reconstruction.id _item_description.description ; The value of _em_3d_reconstruction.id must uniquely identify the 3d reconstruction. ; _item.name '_em_3d_reconstruction.id' _item.category_id em_3d_reconstruction _item.mandatory_code yes _item_type.code code save_ save__em_3d_reconstruction.method _item_description.description ; The algorithm method used for the 3d-reconstruction. ; _item.name '_em_3d_reconstruction.method' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text _item_examples.case 'cross-common lines' save_ save__em_3d_reconstruction.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_3d_reconstruction.citation_id' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_3d_reconstruction.citation_id' _item_linked.parent_name '_citation.id' save_ save__em_3d_reconstruction.details _item_description.description ; Any additional details used in the 3d reconstruction. ; _item.name '_em_3d_reconstruction.details' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text save_ save__em_3d_reconstruction.resolution _item_description.description ; The final resolution (in angstroms)of the 3d reconstruction. ; _item.name '_em_3d_reconstruction.resolution' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__em_3d_reconstruction.resolution_method _item_description.description ; The method used to determine the final resolution of the 3d reconstruction. The Fourier Shell Correlation criterion as a measure of resolution is based on the concept of splitting the (2D) data set into two halves; averaging each and comparing them using the Fourier Ring Correlation (FRC) technique. ; _item.name '_em_3d_reconstruction.resolution_method' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text _item_examples.case 'FSC at 0.5 cut-off' save_ save__em_3d_reconstruction.magnification_calibration _item_description.description ; The magnification calibration method for the 3d reconstruction. ; _item.name '_em_3d_reconstruction.magnification_calibration' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text save_ save__em_3d_reconstruction.ctf_correction_method _item_description.description ; The CTF-correction method. The Contrast Transfer Function CTF compensation for low contrast specimens (e.g. frozen-hydrated), for which phase contrast is the only significant mechanism, then higher defocus levels must be used to achieve any significant transfer, and several images at different focus levels must be combined to complete the information lost from the transfer gaps of any one image. The CTF correction can be applied to each extracted particle separately or to the whole micrograph after digitisation. The simplest level of compensation is to reverse phases at the negative lobes of the CTF. ; _item.name '_em_3d_reconstruction.ctf_correction_method' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text _item_examples.case 'CTF correction of each particle' save_ save__em_3d_reconstruction.nominal_pixel_size _item_description.description ; The nominal pixel size of the projection set of images. ; _item.name '_em_3d_reconstruction.nominal_pixel_size' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code float save_ save__em_3d_reconstruction.actual_pixel_size _item_description.description ; The actual pixel size of projection set of images. ; _item.name '_em_3d_reconstruction.actual_pixel_size' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code float save_ ################### ## EM_3D_FITTING ## ################### save_em_3d_fitting _category.description ; Data items in the 3D_FITTING category record details of the method of fitting atomic coordinates from a PDB file into a 3d-em volume map file ; _category.id em_3d_fitting _category.mandatory_code no loop_ _category_key.name '_em_3d_fitting.id' '_em_3d_fitting.entry_id' loop_ _category_group.id 'em_group' 'inclusive_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_3d_fitting.id 1 _em_3d_fitting.entry_id 1DYL _em_3d_fitting.method AUTOMATIC _em_3d_fitting.target_criteria R-FACTOR _em_3d_fitting.software_name 1 _em_3d_fitting.over_all_b_value . _em_3d_fitting.ref_space REAL _em_3d_fitting.ref_protocol 'RIGID BODY REFINEMENT' _em_3d_fitting.details ; THE CRYSTAL STRUCTURE OF THE CAPSID PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27:345-359 (SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE FOUR INDEPENDENT MONOMER DENSITIES BETWEEN THE INNER LEAFLET OF THE BILAYER AND THE RNA. THESE POSITIONS WERE THEN REFINED BY RIGID BODY REFINEMENT IN REAL SPACE WITH THE PROGRAM EMFIT (CHENG ET AL. 1995, CELL 80, 621-630). THE QUALITY OF THE FIT CAN BE SEEN FROM THE MAP DENSITY WITHIN THE PROTEIN. ALL 4563 ATOMS ARE IN DENSITY OF AT LEAST 4 SIGMA (96.73) ABOVE THE AVERAGE (512.04), 1167 ATOMS ARE IN DENSITY BETWEEN 4 AND 5 SIGMA, 3174 ATOMS ARE IN DENSITY BETWEEN 5 AND 6 SIGMA, AND 222 ATOMS ARE IN DENSTY OF 6 SIGMA OR ABOVE. THE VARIATION IN DENSITY OVER THE FITTED PROTEIN CAN BE VISUALIZED WITH THE PSEUDO TEMPERATURE FACTOR. THE DENSITY VALUE AT EACH ATOM IS GIVEN IN THE 8TH COLUM (USUALLY THE OCCUPANCY) AS THE NUMBER OF STANDARD DEVIATION ABOVE BACKGROUND. COLUMN NINE (USUALLY THE TEMPERATURE FACTOR) CONTAINS THE VALUE OF THE RELATIVE DENSITY WITHIN THE FITTED PROTEIN SCALED LINEARLY SO THAT THE MINIMUM DENSITY IS 100.0 AND THE MAXIMUM DENSITY IS 1.0. THE ATOMS THAT LIE IN THE LOWER DENSITY REGIONS WILL HAVE THE HIGHEST PSEUDO TEMPERATURE FACTORS. ; ; save_ save__em_3d_fitting.id _item_description.description ; The value of _em_3d_fitting.id must uniquely identify a fitting procedure of atomic coordinates into 3dem reconstructed volume map. ; loop_ _item.name _item.category_id _item.mandatory_code '_em_3d_fitting.id' em_3d_fitting yes '_em_3d_fitting_list.3d_fitting_id' em_3d_fitting_list yes loop_ _item_linked.child_name _item_linked.parent_name '_em_3d_fitting_list.3d_fitting_id' '_em_3d_fitting.id' _item_type.code code save_ save__em_3d_fitting.entry_id _item_description.description ; This data item is a pointer to _entry_id in the ENTRY category. ; _item.name '_em_3d_fitting.entry_id' _item.category_id em_3d_fitting _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_3d_fitting.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_3d_fitting.method _item_description.description ; The method used to fit atomic coordinates into the 3dem reconstructed map. ; _item.name '_em_3d_fitting.method' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code line save_ save__em_3d_fitting.target_criteria _item_description.description ; The quality of fit of the atomic coordinates into the 3dem volume map. ; _item.name '_em_3d_fitting.target_criteria' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code text _item_examples.case 'best visual fit using the program O' save_ save__em_3d_fitting.software_name _item_description.description ; This data item is a pointer to _software.name in the category. ; _item.name '_em_3d_fitting.software_name' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code line # _item_linked.child_name '_em_3d_fitting.software_name' # _item_linked.parent_name '_software.name' save_ save__em_3d_fitting.details _item_description.description ; Any additional details regarding fitting of atomic coordinates into the 3d-em volume. ; _item.name '_em_3d_fitting.details' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code text _item_examples.case 'partial' save_ save__em_3d_fitting.overall_b_value _item_description.description ; The overall B (temperature factor) value for the 3d-em volume. ; _item.name '_em_3d_fitting.overall_b_value' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code float save_ save__em_3d_fitting.ref_space _item_description.description ; A flag to indicate whether fitting was carried out in real or reciprocal refinement space. ; _item.name '_em_3d_fitting.ref_space' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value REAL RECIPROCAL save_ save__em_3d_fitting.ref_protocol _item_description.description ; The type of protocol used in the refinement. ; _item.name '_em_3d_fitting.ref_protocol' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code text _item_examples.case 'rigid body' save_ ######################## ## EM_3D_FITTING_LIST ## ######################## save_em_3d_fitting_list _category.description ; Data items in the 3D_FITTING_LIST category lists the methods of fitting atomic coordinates from a PDB file into a 3d-em volume map file ; _category.id em_3d_fitting_list _category.mandatory_code no loop_ _category_key.name '_em_3d_fitting_list.id' '_em_3d_fitting_list.3d_fitting_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_3d_fitting_list.id 1 _em_3d_fitting_list.fitting_id l _em_3d_fitting_list.pdb_entry_id 1VCQ _em_3d_fitting_list.pdb_chain_id . ; save_ save__em_3d_fitting_list.id _item_description.description ; This data item is a unique identifier. ; _item.name '_em_3d_fitting_list.id' _item.category_id em_3d_fitting_list _item.mandatory_code yes _item_type.code code save_ save__em_3d_fitting_list.3d_fitting_id _item_description.description ; The value of _em_3d_fitting_list.3d_fitting_id is a pointer to _em_3d_fitting.id in the 3d_fitting category ; _item.name '_em_3d_fitting_list.3d_fitting_id' _item.mandatory_code yes save_ save__em_3d_fitting_list.pdb_entry_id _item_description.description ; The PDB code for the entry used in fitting. ; _item.name '_em_3d_fitting_list.pdb_entry_id' _item.category_id em_3d_fitting_list _item.mandatory_code no _item_type.code line save_ save__em_3d_fitting_list.pdb_chain_id _item_description.description ; The chain id for the entry used in fitting. ; _item.name '_em_3d_fitting_list.pdb_chain_id' _item.category_id em_3d_fitting_list _item.mandatory_code no _item_type.code code save_ ############################# ## EM_ELECTRON_DIFFRACTION ## ############################# save_em_electron_diffraction _category.description ; Data items in the EM_ELECTRON_DIFFRACTION category record details about the electron diffraction data from the electron crystallography experiment. ; _category.id em_electron_diffraction _category.mandatory_code no loop_ _category_key.name '_em_electron_diffraction.id' '_em_electron_diffraction.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1TUB and laboratory records for the structure corresponding to PDB entry 1TUB ; ; _em_electron_diffraction.entry_id 1TUB _em_electron_diffraction.id 1 _em_electron_diffraction.num_structure_factors 12000 _em_electron_diffraction.num_diff_patterns . _em_electron_diffraction.details . ; save_ save__em_electron_diffraction.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_electron_diffraction.entry_id' _item.category_id em_electron_diffraction _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_electron_diffraction.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_electron_diffraction.id _item_description.description ; The value of _electron_diffraction.id must uniquely identify the electron diffraction experiment. ; _item.name '_em_electron_diffraction.id' _item.category_id em_electron_diffraction _item.mandatory_code yes _item_type.code code save_ save__em_electron_diffraction.num_structure_factors _item_description.description ; The number of structure factors from the electron diffraction experiment. ; _item.name '_em_electron_diffraction.num_structure_factors' _item.category_id em_electron_diffraction _item.mandatory_code no _item_type.code int _item_examples.case '12000' save_ save__em_electron_diffraction.num_diff_patterns _item_description.description ; The number of diffraction patterns used from the electron diffraction experiment. ; _item.name '_em_electron_diffraction.num_diff_patterns' _item.category_id em_electron_diffraction _item.mandatory_code no _item_type.code int save_ save__em_electron_diffraction.details _item_description.description ; Details of the electron diffraction experiment ; _item.name '_em_electron_diffraction.details' _item.category_id em_electron_diffraction _item.mandatory_code yes _item_type.code text loop_ _item_examples.case _item_examples.detail 1 ; THE MODEL WAS DERIVED USING ELECTRON DIFFRACTION AND IMAGE DATA FROM TWO DIMENSIONAL CRYSTALS OF TUBULIN INDUCED BY THE PRESENCE OF ZN++ IONS. WHAT FOLLOWS ARE THE COORDINATES FOR THE AB-TUBULIN DIMER BOUND TO TAXOL AS OBTAINED BY ELECTRON CRYSTALLOGRAPHY OF ZINC-INDUCED SHEETS. THIS IS THE UNREFINED MODEL, BUILT INTO A RAW DENSITY MAP WHERE THE RESOLUTION IN THE PLANE OF THE SHEET WAS 3.7 ANGSTROMS AND THAT PERPENDICULAR TO THE SHEET ABOUT 4.8 ANGSTROMS. THE MODEL DOES NOT CONTAIN MOST OF THE C-TERMINAL RESIDUES OF EITHER MONOMER WHICH WERE DISORDERED IN THE MAP. THE LOOP BETWEEN HELIX H1 AND STRAND S2, AND THAT BETWEEN H2 AND S3 ARE PRESENT FOR COMPLETENESS BUT WERE BUILT INTO VERY WEAK DENSITY. GIVEN THE LIMITED RESOLUTION OF THE MAP, THE CONFORMATION OF THE SIDE CHAINS, ESPECIALLY THOSE CORRESPONDING TO RESIDUES ON THE SURFACE OF THE DIMER, MUST BE TAKEN CAUTIOUSLY. IN ADDITION, BECAUSE THIS IS AN UNREFINED MODEL, CERTAIN GEOMETRY ERRORS MAY STILL BE PRESENT IN THE STRUCTURE. PLEASE TAKE THIS INTO ACCOUNT WHEN INTERPRETING YOUR OWN DATA BASED ON THE PRESENT TUBULIN STRUCTURE. ALTHOUGH THE POSITION OF RESIDUES (WITH THE EXCEPTION OF THOSE IN THE LOOPS MENTIONED ABOVE) SHOULD NOT CHANGE SIGNIFICANTLY UPON REFINEMENT, DRAWING INFORMATION AT THE LEVEL OF SIDE CHAIN CONFORMATION IS CLEARLY NOT ADVISED. FINALLY, PLEASE NOTICE THAT THE TAXOID IN THE MODEL IS THE TAXOL DERIVATIVE TAXOTERE. ; save_ ################################### ## EM_ELECTRON_DIFFRACTION_PHASE ## ################################### save_em_electron_diffraction_phase _category.description ; data items in the em_electron_diffraction_phase category record details about the phase information from the electron diffraction experiment. ; _category.id em_electron_diffraction_phase _category.mandatory_code no loop_ _category_key.name '_em_electron_diffraction_phase.id' '_em_electron_diffraction_phase.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; example 1 - based on pdb entry 1tub and laboratory records for the structure corresponding to pdb entry 1tub ; ; _em_electron_diffraction_phase.entry_id 1TUB _em_electron_diffraction_phase.id 1 _em_electron_diffraction_phase.d_res_low 5.0 _em_electron_diffraction_phase.d_res_high 4.0 _em_electron_diffraction_phase.residual . _em_electron_diffraction_phase.highest_resolution_shell_error . _em_electron_diffraction_phase.overall_error . _em_electron_diffraction_phase.rejection_criteria_error . ; save_ save__em_electron_diffraction_phase.entry_id _item_description.description ; this data item is a pointer to _entry.id in the entry category. ; _item.name '_em_electron_diffraction_phase.entry_id' _item.category_id em_electron_diffraction_phase _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_electron_diffraction_phase.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_electron_diffraction_phase.id _item_description.description ; the value of _electron_diffraction_phase.id must uniquely identify the electron diffraction phase experiment. ; _item.name '_em_electron_diffraction_phase.id' _item.category_id em_electron_diffraction_phase _item.mandatory_code yes _item_type.code code save_ save__em_electron_diffraction_phase.d_res_high _item_description.description ; the highest resolution d-value for the electron diffraction experiment. ; _item.name '_em_electron_diffraction_phase.d_res_high' _item.category_id em_electron_diffraction_phase _item.mandatory_code no _item_type.code int _item_examples.case '5.0' save_ save__em_electron_diffraction_phase.residual _item_description.description ; the phase residual value for the electron diffraction experiment. ; _item.name '_em_electron_diffraction_phase.residual' _item.category_id em_electron_diffraction_phase _item.mandatory_code no _item_type.code int save_ save__em_electron_diffraction_phase.highest_resolution_shell_error _item_description.description ; the highest resolution shell error in degrees. ; _item.name '_em_electron_diffraction_phase.highest_resolution_shell_error' _item.category_id em_electron_diffraction_phase _item.mandatory_code no _item_type.code int save_ save__em_electron_diffraction_phase.overall_error _item_description.description ; the overall phase error in degrees. ; _item.name '_em_electron_diffraction_phase.overall_error' _item.category_id em_electron_diffraction_phase _item.mandatory_code no _item_type.code int save_ save__em_electron_diffraction_phase.rejection_criteria_error _item_description.description ; the rejection criteria (phase error) in degrees. ; _item.name '_em_electron_diffraction_phase.rejection_criteria_error' _item.category_id em_electron_diffraction_phase _item.mandatory_code no _item_type.code int save_ ##################################### ## EM_ELECTRON_DIFFRACTION_PATTERN ## ##################################### save_em_electron_diffraction_pattern _category.description ; data items in the em_electron_diffraction_pattern category record details about the pattern information from the electron diffraction experiment. ; _category.id em_electron_diffraction_pattern _category.mandatory_code no loop_ _category_key.name '_em_electron_diffraction_pattern.id' '_em_electron_diffraction_pattern.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; example 1 - based on pdb entry 1tub and laboratory records for the structure corresponding to pdb entry 1tub ; ; _em_electron_diffraction_pattern.entry_id 1TUB _em_electron_diffraction_pattern.id 1 _em_electron_diffraction_pattern.num_patterns_by_tilt_angle 1 _em_electron_diffraction_pattern.num_images_by_tilt_angle 4 _em_electron_diffraction_pattern.tilt_angle . ; save_ save__em_electron_diffraction_pattern.entry_id _item_description.description ; this data item is a pointer to _entry.id in the entry category. ; _item.name '_em_electron_diffraction_pattern.entry_id' _item.category_id em_electron_diffraction_pattern _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_electron_diffraction_pattern.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_electron_diffraction_pattern.id _item_description.description ; the value of _electron_diffraction_pattern.id must uniquely identify the electron diffraction pattern experiment. ; _item.name '_em_electron_diffraction_pattern.id' _item.category_id em_electron_diffraction_pattern _item.mandatory_code yes _item_type.code code save_ save__em_electron_diffraction_pattern.num_patterns_by_tilt_angle _item_description.description ; the number of diffraction patterns by tilt angle. ; _item.name '_em_electron_diffraction_pattern.num_patterns_by_tilt_angle' _item.category_id em_electron_diffraction_pattern _item.mandatory_code no _item_type.code int _item_examples.case '1' save_ save__em_electron_diffraction_pattern.num_images_by_tilt_angle _item_description.description ; the number of images by tilt angle. ; _item.name '_em_electron_diffraction_pattern.num_images_by_tilt_angle' _item.category_id em_electron_diffraction_pattern _item.mandatory_code no _item_type.code int _item_examples.case '4' save_ save__em_electron_diffraction_pattern.tilt_angle _item_description.description ; the tilt angle at which the diffraction pattern was obtained. ; _item.name '_em_electron_diffraction_pattern.tilt_angle' _item.category_id em_electron_diffraction_pattern _item.mandatory_code no _item_type.code int save_ ### EOF mmcif_iims-def-2.dic