########################################################################### # # File: mmcif_em.dic # Date: Fri May 30 15:35:25 EDT 2008 # # Created from files in CVS module dict-mmcif_em.dic unless noted: # mmcif_em-header.dic # mmcif_em-data.dic # mmcif_em-def-1.dic # ########################################################################### ########################################################################### # # File: mmcif_em-header.dic # # PDB Extension Dictionary for 3-Dimensional # Electron Microscopy # # This dictionary supplements the contents of the mmCIF data dictionary # with additional data items that may be required to represent # structure and experimental data produced by 3-dimensional electron # microscopy experiments. # # Extensions are based on community suggestions and encoded by # Richard Newman and Kim Henrick at the Molecular Structure Database # (MSD) Group/EBI and John Westbrook at PDB RCSB. # # # # Header Section # ############################################################################## data_mmcif_em.dic _datablock.id mmcif_em.dic _datablock.description ; This data block holds the mmCIF data definitions with extensions for 3-dimensional electron microscopy. ; _dictionary.title mmcif_em.dic _dictionary.datablock_id mmcif_em.dic _dictionary.version 0.014 # loop_ _dictionary_history.version _dictionary_history.update _dictionary_history.revision 0.001 2001-09-21 ; Initial version. ; 0.002 2004-04-15 ; Changes: (jdw) + Added partitioning and dictionary revision history. + Fix syntax errors in category examples. + Added missing units. ; 0.003 2004-10-10 ; Changes: (jdw) + Adjust enumerations ; 0.004 2004-11-03 ; Changes: + Reflects revisions from EM Workshop Oct 2004. ; 0.005 2004-12-04 ; Changes: + Added em_electron_diffraction, em_electron_diffraction_phasing, and em_electron_diffraction_pattern + Miscellaneous corrections. ; 0.006 2005-06-01 ; Changes: (jdw) + Add category groups + Add changes proposed by EM Workshop participants. ; 0.007 2005-06-09 ; Changes: (jdw) + Reorganize em_sample_description_group + Reorganize em_data_collection_group + Reorganize em_image_selection_group + Detailed particle list categories temporarily removed from this version. ; 0.008 2005-06-09 ; Changes: (jdw) + revise category keys in em_image_selection group ; 0.009 2005-07-13 ; Changes: (jdw) + Added Cathy Lawson's revised definitions and examples. ; 0.010 2005-07-28 ; Changes: (jdw) + Implemented changes recommended by Wah Chiu, Matt Baker, and Cathy Lawson. ; 0.011 2005-07-29 ; Changes: (jdw) + Corrections to v0.010 + Implemented changes recommended by Bridget Carragher and Ron Milligan ; 0.012 2005-08-23 ; Changes: (jdw) + Remove non-ascii characters from description text. ; 0.013 2005-10-14 ; Changes: (jdw) + Remove more special characters from enumerations. + Renamed iims -> em ; 0.014 2007-11-19 ; Changes: (jdw/cl) + update example for category em_array_formation + miscellaneous corrections ; ### EOF mmcif_em-header.dic ########################################################################### # # File: mmcif_em-data.dic # # PDB Extension Dictionary for 3-Dimensional # Electron Microscopy # # Data Section # # ########################################################################### ################## ## SUB_CATEGORY ## ################## loop_ _sub_category.id _sub_category.description 'cartesian_coordinate' ; The collection of x, y, and z components of a position specified with reference to a Cartesian (orthogonal angstrom) coordinate system. ; 'cartesian_coordinate_esd' ; The collection of estimated standard deviations of the x, y, and z components of a position specified with reference to a Cartesian (orthogonal angstrom) coordinate system. ; 'fractional_coordinate' ; The collection of x, y, and z components of a position specified with reference to unit cell directions. ; 'fractional_coordinate_esd' ; The collection of estimated standard deviations of the x, y, and z components of a position specified with reference to unit cell directions. ; 'matrix' ; The collection of elements of a matrix. ; miller_index ; The collection of h, k, and l components of the Miller index of a reflection. ; 'cell_length' ; The collection of a, b, and c axis lengths of a unit cell. ; 'cell_length_esd' ; The collection of estimated standard deviations of the a, b, and c axis lengths of a unit cell. ; 'cell_angle' ; The collection of alpha, beta, and gamma angles of a unit cell. ; 'cell_angle_esd' ; The collection of estimated standard deviations of the alpha, beta, and gamma angles of a unit cell. ; 'mm_atom_site_auth_label' ; The collection of asym id, atom id, comp id and seq id components of an author's alternative specification for a macromolecular atom site. ; 'mm_atom_site_label' ; The collection of alt id, asym id, atom id, comp id and seq id components of the label for a macromolecular atom site. ; 'vector' ; The collection of elements of a vector. ; ######################### ## CATEGORY_GROUP_LIST ## ######################### loop_ _category_group_list.id _category_group_list.parent_id _category_group_list.description 'inclusive_group' . ; Categories that belong to the macromolecular dictionary. ; 'em_group' . ; Categories that belong to the Electron Microscopy dictionary. ; 'em_sample_description_group' . ; Categories that belong to the Electron Microscopy sample description. ; 'em_biochemical_preparation_group' . ; Categories that belong to the Electron Microscopy sample preparation. ; 'em_specimen_preparation_group' . ; Categories that belong to the Electron Microscopy specimen preparation. ; 'em_data_collection_group' . ; Categories that belong to the Electron Microscopy data collection. ; 'em_image_selection_group' . ; Categories that describing the selection of Electron Microscopy images. ; 'em_reconstruction_group' . ; Categories that belong to the Electron Microscopy image reconstruction. ; 'em_structure_analysis_group' . ; Categories that belong to the Electron Microscopy structure analysis. ; 'em_map_group' . ; Categories that belong to the Electron Microscopy map description. ; 'em_tomography_group' . ; Categories that belong to the Electron Microscopy tomography. ; 'em_single_particle_group' . ; Categories that describe the properties of single particles in EM studies. ; 'em_helical_group' . ; Categories that describe the properties of helical particles in EM studies. ; 'em_2D_crystal_group' . ; Categories that describe the properties of 2D crystals in EM studies. ; #################### ## 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 the version 0.12 of Richard Stallman's # GNU regular expression libary in POSIX mode. # # # For some data items, a standard syntax is assumed. The syntax is # described for each data item in the dictionary, but is summarized here: # # Names: The family name(s) followed by a comma, precedes the first # name(s) or initial(s). # # Telephone numbers: # The international code is given in brackets and any extension # number is preceded by 'ext'. # # Dates: In the form yyyy-mm-dd. # ############################################################################## 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()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; text item types / multi-line text ... ; int numb '-?[0-9]+' ; int item types are the subset of numbers that are the negative or positive integers. ; float numb '-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?' ; int item types are the subset of numbers that are the floating numbers. ; name uchar '_[_A-Za-z0-9]+\.[][_A-Za-z0-9%-]+' ; name item types take the form... ; idname uchar '[_A-Za-z0-9]+' ; idname item types take the form... ; any char '.*' ; A catch all for items that may take any form... ; yyyy-mm-dd char '[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]' ; Standard format for CIF dates. ; uchar3 uchar '[+]?[A-Za-z0-9][A-Za-z0-9][A-Za-z0-9]' ; data item for 3 character codes ; uchar1 uchar '[+]?[A-Za-z0-9]' ; data item for 1 character codes ; symop char '([1-9]|[1-9][0-9]|1[0-8][0-9]|19[0-2])(_[1-9][1-9][1-9])?' ; symop item types take the form n_klm, where n refers to the symmetry operation that is applied to the coordinates in the ATOM_SITE category identified by _atom_site_label. It must match a number given in _symmetry_equiv_pos_site_id. k, l, and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used. These translations (x,y,z) are related to (k,l,m) by k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; atcode char '[][ _(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; Character data type for atom names ... ; ##################### ## ITEM_UNITS_LIST ## ##################### loop_ _item_units_list.code _item_units_list.detail # 'centimetres' 'centimetres (meters * 10^( -2))' 'millimetres' 'millimetres (meters * 10^( -3))' 'nanometres' 'nanometres (meters * 10^( -9))' 'angstroms' 'angstroms (meters * 10^(-10))' 'picometres' 'picometres (meters * 10^(-12))' 'femtometres' 'femtometres (meters * 10^(-15))' # 'reciprocal_centimetres' 'reciprocal centimetres (meters * 10^( -2)^-1)' 'reciprocal_millimetres' 'reciprocal millimetres (meters * 10^( -3)^-1)' 'reciprocal_nanometres' 'reciprocal nanometres (meters * 10^( -9)^-1)' 'reciprocal_angstroms' 'reciprocal angstroms (meters * 10^(-10)^-1)' 'reciprocal_picometres' 'reciprocal picometres (meters * 10^(-12)^-1)' # 'nanometres_squared' 'nanometres squared (meters * 10^( -9))^2' 'angstroms_squared' 'angstroms squared (meters * 10^(-10))^2' '8pi2_angstroms_squared' '8pi^2 * angstroms squared (meters * 10^(-10))^2' 'picometres_squared' 'picometres squared (meters * 10^(-12))^2' # 'nanometres_cubed' 'nanometres cubed (meters * 10^( -9))^3' 'angstroms_cubed' 'angstroms cubed (meters * 10^(-10))^3' 'picometres_cubed' 'picometres cubed (meters * 10^(-12))^3' # 'kilopascals' 'kilopascals' 'gigapascals' 'gigapascals' # 'hours' 'hours' 'minutes' 'minutes' 'seconds' 'seconds' 'microseconds' 'microseconds' # 'degrees' 'degrees (of arc)' # 'degrees_per_minute' 'degrees (of arc) per minute' # 'celsius' 'degrees (of temperature) Celsius' 'kelvins' 'degrees (of temperature) Kelvin' # 'electrons' 'electrons' # 'electrons_squared' 'electrons squared' # 'electrons_per_nanometres_cubed' ; electrons per nanometres cubed (meters * 10^( -9))^3 ; 'electrons_per_angstroms_cubed' ; electrons per angstroms cubed (meters * 10^(-10))^3 ; 'electrons_per_picometres_cubed' ; electrons per picometres cubed (meters * 10^(-12))^3 ; 'kilowatts' 'kilowatts' 'milliamperes' 'milliamperes' 'kilovolts' 'kilovolts' # 'arbitrary' ; arbitrary system of units. ; # 'megadaltons' 'megadaltons' 'daltons' 'daltons' 'microns_squared' 'microns squared' 'microns' 'microns' # 'millimeters' 'millimeters' 'electrons_angstrom_squared' 'electrons square angstrom' 'electron_volts' 'electron volts' 'millimolar' 'millimolar' 'mg_per_ml' 'milligram per milliliter' loop_ _item_units_conversion.from_code _item_units_conversion.to_code _item_units_conversion.operator _item_units_conversion.factor ### 'centimetres' 'millimetres' '*' 1.0E+01 'centimetres' 'nanometres' '*' 1.0E+07 'centimetres' 'angstroms' '*' 1.0E+08 'centimetres' 'picometres' '*' 1.0E+10 'centimetres' 'femtometres' '*' 1.0E+13 # 'millimetres' 'centimetres' '*' 1.0E-01 'millimetres' 'nanometres' '*' 1.0E+06 'millimetres' 'angstroms' '*' 1.0E+07 'millimetres' 'picometres' '*' 1.0E+09 'millimetres' 'femtometres' '*' 1.0E+12 # 'nanometres' 'centimetres' '*' 1.0E-07 'nanometres' 'millimetres' '*' 1.0E-06 'nanometres' 'angstroms' '*' 1.0E+01 'nanometres' 'picometres' '*' 1.0E+03 'nanometres' 'femtometres' '*' 1.0E+06 # 'angstroms' 'centimetres' '*' 1.0E-08 'angstroms' 'millimetres' '*' 1.0E-07 'angstroms' 'nanometres' '*' 1.0E-01 'angstroms' 'picometres' '*' 1.0E+02 'angstroms' 'femtometres' '*' 1.0E+05 # 'picometres' 'centimetres' '*' 1.0E-10 'picometres' 'millimetres' '*' 1.0E-09 'picometres' 'nanometres' '*' 1.0E-03 'picometres' 'angstroms' '*' 1.0E-02 'picometres' 'femtometres' '*' 1.0E+03 # 'femtometres' 'centimetres' '*' 1.0E-13 'femtometres' 'millimetres' '*' 1.0E-12 'femtometres' 'nanometres' '*' 1.0E-06 'femtometres' 'angstroms' '*' 1.0E-05 'femtometres' 'picometres' '*' 1.0E-03 ### 'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01 'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07 'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08 'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10 # 'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01 'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06 'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07 'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09 # 'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07 'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06 'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01 'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03 # 'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08 'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07 'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01 'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02 # 'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10 'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09 'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03 'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01 ### 'nanometres_squared' 'angstroms_squared' '*' 1.0E+02 'nanometres_squared' 'picometres_squared' '*' 1.0E+06 # 'angstroms_squared' 'nanometres_squared' '*' 1.0E-02 'angstroms_squared' 'picometres_squared' '*' 1.0E+04 'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568 # 'picometres_squared' 'nanometres_squared' '*' 1.0E-06 'picometres_squared' 'angstroms_squared' '*' 1.0E-04 ### 'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03 'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09 # 'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03 'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06 # 'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09 'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06 ### 'kilopascals' 'gigapascals' '*' 1.0E-06 'gigapascals' 'kilopascals' '*' 1.0E+06 ### 'hours' 'minutes' '*' 6.0E+01 'hours' 'seconds' '*' 3.6E+03 'hours' 'microseconds' '*' 3.6E+09 # 'minutes' 'hours' '/' 6.0E+01 'minutes' 'seconds' '*' 6.0E+01 'minutes' 'microseconds' '*' 6.0E+07 # 'seconds' 'hours' '/' 3.6E+03 'seconds' 'minutes' '/' 6.0E+01 'seconds' 'microseconds' '*' 1.0E+06 # 'microseconds' 'hours' '/' 3.6E+09 'microseconds' 'minutes' '/' 6.0E+07 'microseconds' 'seconds' '/' 1.0E+06 ### 'celsius' 'kelvins' '-' 273.0 'kelvins' 'celsius' '+' 273.0 ### 'electrons_per_nanometres_cubed' 'electrons_per_angstroms_cubed' '*' 1.0E-03 'electrons_per_nanometres_cubed' 'electrons_per_picometres_cubed' '*' 1.0E-09 # 'electrons_per_angstroms_cubed' 'electrons_per_nanometres_cubed' '*' 1.0E+03 'electrons_per_angstroms_cubed' 'electrons_per_picometres_cubed' '*' 1.0E-06 # 'electrons_per_picometres_cubed' 'electrons_per_nanometres_cubed' '*' 1.0E+09 'electrons_per_picometres_cubed' 'electrons_per_angstroms_cubed' '*' 1.0E+06 ### ### EOF mmcif_em-data.dic ########################################################################## # # File: mmcif_em-def-1.dic # # PDB Extension Dictionary for 3-Dimensional # Electron Microscopy # # Definition Section v1 # # ########################################################################### ############### ## EM_ENTRY ## ############### save_em_entry _category.description ; The EM_ENTRY category records a unique identifier for the data block describing an EM experiment. ; _category.id em_entry _category.mandatory_code yes _category_key.name '_em_entry.id' loop_ _category_group.id 'inclusive_group' 'em_group' save_ save__em_entry.id _item_description.description ; The value of _em_entry.id identifies the data block. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_em_entry.id' _item.category_id em_entry _item.mandatory_code yes _item_type.code code _item_examples.case RDV2 save_ # ############ # EM_EXPTL # ############ save_em_exptl _category.description ; Data items in the em_assembly category record basic information about the method used to produce the EM map. ; _category.id em_exptl _category.mandatory_code yes loop_ _category_key.name '_em_exptl.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_sample_description_group' loop_ _category_examples.detail _category_examples.case 'based on PDB entry 1DGI' ; _em_exptl.entry_id 1DGI _em_exptl.reconstruction_method 'SINGLE PARTICLE' _em_exptl.resolution_published 22.0 ; save_ save__em_exptl.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_exptl.entry_id' _item.category_id em_exptl _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_exptl.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_exptl.reconstruction_method _item_description.description ; A description of the method used in the EM experiment to generate the map. SINGLE PARTICLE: reconstruction of asymmetric particles or particles with point symmetry, e.g., ribosome, GroEL, icosahedral phage FILAMENT: reconstruction of particles with helical symmetry, e.g., filamentous phage, helical acetylcholine receptor crystal 2D CRYSTAL: reconstruction of a 2D lattice, e.g., aquoporin crystal, bacteriorhodopsin crystal 3D CRYSTAL: reconstruction of a 3D lattice, e.g., yeast peroxisome crystal, acrosomal bundle INDIVIDUAL STRUCTURE (TOMOGRAM): reconstruction of a single object, e.g., bacterial cell, desmosomal knot MULTIPLE SELECTION: multiple methods used. ; _item.name '_em_exptl.reconstruction_method' _item.category_id em_exptl _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value 'SINGLE PARTICLE' 'FILAMENT' '2D CRYSTAL' '3D CRYSTAL' 'INDIVIDUAL STRUCTURE' 'MULTIPLE SELECTION' save_ save__em_exptl.resolution_high _item_description.description ; The author determined highest resolution of the reconstruction ; _item.name '_em_exptl.resolution_high' _item.category_id em_exptl _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__em_exptl.resolution_low _item_description.description ; The author determined lowest resolution of the reconstruction ; _item.name '_em_exptl.resolution_low' _item.category_id em_exptl _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__em_exptl.resolution_published _item_description.description ; The author determined resolution of the reconstruction ; _item.name '_em_exptl.resolution_published' _item.category_id em_exptl _item.mandatory_code yes _item_type.code float _item_units.code angstroms save_ ################# ## EM_ASSEMBLY ## ################# save_em_assembly _category.description ; Data items in the em_assembly category record basic information about the assembly represented by the EM map. ; _category.id em_assembly _category.mandatory_code yes loop_ _category_key.name '_em_assembly.id' '_em_assembly.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_sample_description_group' loop_ _category_examples.detail _category_examples.case 'based on PDB entry 1DGI' ; _em_assembly.id 1 _em_assembly.entry_id 1DGI _em_assembly.name 'Poliovirus-CD155' _em_assembly.composition 'virus-receptor complex' _em_assembly.num_components 2 _em_assembly.array no _em_assembly.superstructure no ; 'based on PDB entry 2BG9' ; _em_assembly.id 1 _em_assembly.entry_id 2BG9 _em_assembly.name 'Acetylcholine receptor, Torpedo postsynaptic membrane' _em_assembly.composition 'integral membrane receptor' _em_assembly.num_components 1 _em_assembly.array yes _em_assembly.superstructure yes ; save_ save__em_assembly.id _item_description.description ; The value of _em_assembly.id must uniquely identify the EM experiment. ; _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 biological assembly ; _item.name '_em_assembly.name' _item.category_id em_assembly _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'helical crystals of acetylcholine receptor' 'poliovirus - CD155 receptor complex' save_ save__em_assembly.composition _item_description.description ; The known composition of the sample. ; _item.name '_em_assembly.composition' _item.category_id em_assembly _item.mandatory_code no _item_type.code line save_ save__em_assembly.details _item_description.description ; Any additional details about the assembly. ; _item.name '_em_assembly.details' _item.category_id em_assembly _item.mandatory_code no _item_type.code text save_ #--- next 3 items required to dynamically generate web input pages first # 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.array _item_description.description ; A flag to indicate whether the imaged assembly is part of a regular array, e.g, a 2D or helical crystal. ; _item.name '_em_assembly.array' _item.category_id em_assembly _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value YES NO save_ save__em_assembly.superstructure _item_description.description ; A flag to indicate whether the imaged assembly is part of a larger structure, e.g., a membrane, virus, or cell. ; _item.name '_em_assembly.superstructure' _item.category_id em_assembly _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value YES NO save_ ######################## ## EM_ENTITY_ASSEMBLY ## ######################## save_em_entity_assembly _category.description ; The EM_ENTITY_ASSEMBLY category defines a hierarchy-independent list of assemblies relevant to the EM experiment. The recommended convention is that the imaged assembly, defined in the category EM_ASSEMBLY, is listed first. Components, arrays and superstructures of the assembly are also described. The hierarchy independence enables descriptions of symmetry, sample preparation, particle selection, and map masks at multiple levels. ; _category.id em_entity_assembly _category.mandatory_code no loop_ _category_key.name '_em_entity_assembly.id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_sample_description_group' loop_ _category_examples.detail _category_examples.case 'based on PDB entry 1DGI' ; loop_ _em_entity_assembly.id _em_entity_assembly.assembly_id _em_entity_assembly.type _em_entity_assembly.symmetry_type _em_entity_assembly.name 1 1 'COMPLEX ASSEMBLY' 'point symmetry' 'poliovirus-CD155 complex' 2 1 VIRUS 'point symmetry' 'poliovirus' 3 1 PROTEIN 'asymmetric' 'CD155 receptor' ; 'based on PDB entry 2BG9' ; loop_ _em_entity_assembly.id _em_entity_assembly.assembly_id _em_entity_assembly.type _em_entity_assembly.symmetry_type _em_entity_assembly.name 1 1 PROTEIN 'asymmetric' 'acetylcholine receptor' 2 1 MEMBRANE . 'torpedo post-synaptic membrane' 3 1 ARRAY 'helical' 'helical crystal' ; save_ save__em_entity_assembly.id _item_description.description ; The value of _em_entity_assembly.id must uniquely identify the assembly, component, or superstructure. ; _item.name '_em_entity_assembly.id' _item.category_id em_entity_assembly _item.mandatory_code yes _item_type.code code save_ save__em_entity_assembly.assembly_id _item_description.description ; This data item is a pointer to _em_assembly.id in the em_assembly category. ; _item.name '_em_entity_assembly.assembly_id' _item.category_id em_entity_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_entity_assembly.type _item_description.description ; A description of the biological structure type of the assembly, component, or superstructure. For assemblies containing multiple components, use 'COMPLEX ASSEMBLY'. ; _item.name '_em_entity_assembly.type' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value 'COMPLEX ASSEMBLY' ARRAY CELL MEMBRANE 'CELLULAR COMPONENT' VIRUS PROTEIN 'NUCLEIC ACID' LIPID CARBOHYDRATE LIGAND LABEL OTHER save_ save__em_entity_assembly.symmetry_type _item_description.description ; The type of symmetry of the assembly, component or superstructure. ; _item.name '_em_entity_assembly.symmetry_type' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail asymmetric 'object with no internal symmetry' 'point' 'point symmetry object' helical 'helix/filament' 2D '2D crystal' 3D '3D crystal' 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.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.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_ 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.pdbx_organism_scientific _item_description.description ; The species of the natural organism from which the component was obtained. ; _item.name '_em_entity_assembly.pdbx_organism_scientific' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_em_entity_assembly.ebi_organism_scientific' _item_aliases.dictionary 'mmcif_iims.dic' _item_aliases.version 1.0 save_ save__em_entity_assembly.pdbx_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.pdbx_organism_common' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_em_entity_assembly.ebi_organism_common' _item_aliases.dictionary 'mmcif_iims.dic' _item_aliases.version 1.0 save_ save__em_entity_assembly.pdbx_strain _item_description.description ; The strain of the natural organism from which the component was obtained, if relevant. ; _item.name '_em_entity_assembly.pdbx_strain' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'DH5a' 'BMH 71-18' _item_aliases.alias_name '_em_entity_assembly.ebi_strain' _item_aliases.dictionary 'mmcif_iims.dic' _item_aliases.version 1.0 save_ save__em_entity_assembly.pdbx_tissue _item_description.description ; The tissue of the natural organism from which the component was obtained. ; _item.name '_em_entity_assembly.pdbx_tissue' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'heart' 'liver' 'eye lens' _item_aliases.alias_name '_em_entity_assembly.ebi_tissue' _item_aliases.dictionary 'mmcif_iims.dic' _item_aliases.version 1.0 save_ save__em_entity_assembly.pdbx_cell _item_description.description ; The cell from which the component was obtained. ; _item.name '_em_entity_assembly.pdbx_cell' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'CHO' 'HELA' '3T3' _item_aliases.alias_name '_em_entity_assembly.ebi_cell' _item_aliases.dictionary 'mmcif_iims.dic' _item_aliases.version 1.0 save_ save__em_entity_assembly.pdbx_organelle _item_description.description ; The organelle from which the component was obtained. ; _item.name '_em_entity_assembly.pdbx_organelle' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'golgi' 'mitochondrion' 'cytoskeleton' _item_aliases.alias_name '_em_entity_assembly.ebi_organelle' _item_aliases.dictionary 'mmcif_iims.dic' _item_aliases.version 1.0 save_ save__em_entity_assembly.pdbx_cellular_location _item_description.description ; The cellular location of the component. ; _item.name '_em_entity_assembly.pdbx_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' _item_aliases.alias_name '_em_entity_assembly.ebi_cellular_location' _item_aliases.dictionary 'mmcif_iims.dic' _item_aliases.version 1.0 save_ save__em_entity_assembly.pdbx_engineered _item_description.description ; A flag to indicate whether the component is engineered. ; _item.name '_em_entity_assembly.pdbx_engineered' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value YES NO _item_aliases.alias_name '_em_entity_assembly.ebi_engineered' _item_aliases.dictionary 'mmcif_iims.dic' _item_aliases.version 1.0 save_ save__em_entity_assembly.pdbx_expression_system _item_description.description ; The expression system used to produce the component. ; _item.name '_em_entity_assembly.pdbx_expression_system' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'eschericia coli' 'saccharomyces cerevisiae' _item_aliases.alias_name '_em_entity_assembly.ebi_expression_system' _item_aliases.dictionary 'mmcif_iims.dic' _item_aliases.version 1.0 save_ save__em_entity_assembly.pdbx_expression_system_plasmid _item_description.description ; The plasmid used in the expression system used to produce the component. ; _item.name '_em_entity_assembly.pdbx_expression_system_plasmid' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'pBR322' 'pMB9' _item_aliases.alias_name '_em_entity_assembly.ebi_expression_system_plasmid' _item_aliases.dictionary 'mmcif_iims.dic' _item_aliases.version 1.0 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 molecular entities within the assembly. ; _category.id em_entity_assembly_list _category.mandatory_code no loop_ _category_key.name '_em_entity_assembly_list.assembly_id' '_em_entity_assembly_list.id' '_em_entity_assembly_list.entity_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_sample_description_group' loop_ _category_examples.detail _category_examples.case 'based on PDB entry 1DGI' ; loop_ _em_entity_assembly_list.id _em_entity_assembly_list.assembly_id _em_entity_assembly_list.entity_id _em_entity_assembly_list.number_of_copies VP1 1 1 60 VP2 1 2 60 VP3 1 3 60 VP4 1 4 60 CD155frag 1 5 60 ; 'based on PDB entry 2BG9' ; loop_ _em_entity_assembly_list.id _em_entity_assembly_list.assembly_id _em_entity_assembly_list.entity_id _em_entity_assembly_list.number_of_copies alpha 1 1 2 beta 1 2 1 gamma 1 3 1 delta 1 4 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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.assembly_id _item_description.description ; This data item is a pointer to _em_assembly.id in the EM_ASSEMBLY category. ; _item.name '_em_entity_assembly_list.assembly_id' _item.category_id em_entity_assembly_list _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_entity_assembly_list.assembly_id' _item_linked.parent_name '_em_assembly.id' save_ save__em_entity_assembly_list.details _item_description.description ; The oligomeric state of the entity. ; _item.name '_em_entity_assembly_list.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 within the assembly. ; _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_ save__em_entity_assembly_list.mol_wt _item_description.description ; The value (in daltons) of the molecular weight of each component of the assembly determined by _em_entity_assembly_list.mol_wt_method. ; _item.name '_em_entity_assembly_list.mol_wt' _item.category_id em_entity_assembly_list _item.mandatory_code no _item_type.code float _item_units.code daltons save_ save__em_entity_assembly_list.mol_wt_method _item_description.description ; The method used in determining the molecular weight. ; _item.name '_em_entity_assembly_list.mol_wt_method' _item.category_id em_entity_assembly_list _item.mandatory_code no _item_type.code text save_ ############################### ## EM_ENTITY_ASSEMBLY_MOL_WT ## ############################### save_em_entity_assembly_mol_wt _category.description ; Data items in the EM_ENTITY_ASSEMBLY_MOL_WT category record details of the molecular weight of structural elements in each component. ; _category.id em_entity_assembly_mol_wt _category.mandatory_code no loop_ _category_key.name '_em_entity_assembly_mol_wt.id' '_em_entity_assembly_mol_wt.entity_assembly_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_sample_description_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - microtubule ; ; loop_ _em_entity_assembly_mol_wt.id _em_entity_assembly_mol_wt.entity_assembly_id _em_entity_assembly_mol_wt.mol_wt _em_entity_assembly_mol_wt.mol_wt_method _em_entity_assembly_mol_wt.details 1 1 12000 Calculated 'predicted from gene sequence' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__em_entity_assembly_mol_wt.entity_assembly_id _item_description.description ; The value of _em_entity_assembly_mol_wt.entity_assembly_id identifies a component defined in the EM_ENTITY_ASSEMBLY category. This is a pointer to _em_entity_assembly.id. ; _item.name '_em_entity_assembly_mol_wt.entity_assembly_id' _item.category_id em_entity_assembly_mol_wt _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_entity_assembly_mol_wt.entity_assembly_id' _item_linked.parent_name '_em_entity_assembly.id' save_ save__em_entity_assembly_mol_wt.id _item_description.description ; The value of _em_entity_assembly_mol_wt.id must uniquely identify the molecular weight value provided for each component. ; _item.name '_em_entity_assembly_mol_wt.id' _item.category_id em_entity_assembly_mol_wt _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_entity_assembly_mol_wt.id' _item_linked.parent_name '_em_entity_assembly_list.id' save_ save__em_entity_assembly_mol_wt.mol_wt _item_description.description ; The value (in megadaltons) of the experimentally determined molecular weight of each component of the assembly. ; _item.name '_em_entity_assembly_mol_wt.mol_wt' _item.category_id em_entity_assembly_mol_wt _item.mandatory_code no _item_type.code float _item_units.code megadaltons save_ save__em_entity_assembly_mol_wt.mol_wt_method _item_description.description ; The method used to determine the molecular weight. ; _item.name '_em_entity_assembly_mol_wt.mol_wt_method' _item.category_id em_entity_assembly_mol_wt _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value 'calculated' 'SDS-PAGE' 'size exclusion' 'mass spectrometry' 'STEM' 'other' save_ save__em_entity_assembly_mol_wt.details _item_description.description ; Details of the method used to determine the molecular weight. ; _item.name '_em_entity_assembly_mol_wt.details' _item.category_id em_entity_assembly_mol_wt _item.mandatory_code no _item_type.code text _item_examples.case ; Scanning Transmission Electron Microscopy Mass Measurement-- PM28 isoforms solubilized in OTG were adsorbed for 1 min to glow discharged thin carbon films supported by a thick fenestrated carbon layer (directly after cation-exchange chromatography). The gold-plated copper grids were then washed on 8 drops of quartz double-distilled water and were freeze-dried at -80C overnight in the microscope. For mass analysis, annular dark-field images were recorded in a STEM (VG-HB5) at 80 kV and doses of 325 +/- 35 electrons/nm2. Digital acquisition of the images and microscope parameters, system calibration, and mass analysis were carried out as described previously. The total experimental error was calculated as the standard error of the mean, plus 5% of the measured particle mass to account for the absolute calibration uncertainty. ; save_ ## ############################### ## EM_ENTITY_ASSEMBLY_MOL_WT ## ############################### save_em_entity_assembly_mol_wt _category.description ; Data items in the EM_ENTITY_ASSEMBLY_MOL_WT category record details of the molecular weight of structural elements in each component. ; _category.id em_entity_assembly_mol_wt _category.mandatory_code no loop_ _category_key.name '_em_entity_assembly_mol_wt.id' '_em_entity_assembly_mol_wt.entity_assembly_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_sample_description_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - microtubule ; ; loop_ _em_entity_assembly_mol_wt.id _em_entity_assembly_mol_wt.entity_assembly_id _em_entity_assembly_mol_wt.mol_wt _em_entity_assembly_mol_wt.mol_wt_method _em_entity_assembly_mol_wt.details 1 1 12000 Calculated 'predicted from gene sequence' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__em_entity_assembly_mol_wt.entity_assembly_id _item_description.description ; The value of _em_entity_assembly_mol_wt.entity_assembly_id identifies a component in the EM_ENTITY_ASSEMBLY category. This is a pointer to _em_entity_assembly.id. ; _item.name '_em_entity_assembly_mol_wt.entity_assembly_id' _item.category_id em_entity_assembly_mol_wt _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_entity_assembly_mol_wt.entity_assembly_id' _item_linked.parent_name '_em_entity_assembly.id' save_ save__em_entity_assembly_mol_wt.id _item_description.description ; The value of _em_entity_assembly_mol_wt.id must uniquely identifies the molecular weight value provided for each component. ; _item.name '_em_entity_assembly_mol_wt.id' _item.category_id em_entity_assembly_mol_wt _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_entity_assembly_mol_wt.id' _item_linked.parent_name '_em_entity_assembly_list.id' save_ save__em_entity_assembly_mol_wt.mol_wt _item_description.description ; The value (in megadaltons) of the experimentally determined molecular weight of each component of the assembly. ; _item.name '_em_entity_assembly_mol_wt.mol_wt' _item.category_id em_entity_assembly_mol_wt _item.mandatory_code no _item_type.code float _item_units.code megadaltons save_ save__em_entity_assembly_mol_wt.mol_wt_method _item_description.description ; The method used to determine the molecular weight. ; _item.name '_em_entity_assembly_mol_wt.mol_wt_method' _item.category_id em_entity_assembly_mol_wt _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value 'calculated' 'SDS-PAGE' 'size exclusion' 'mass spectrometry' 'STEM' 'other' save_ save__em_entity_assembly_mol_wt.details _item_description.description ; Details of the method used to determine the molecular weight. ; _item.name '_em_entity_assembly_mol_wt.details' _item.category_id em_entity_assembly_mol_wt _item.mandatory_code no _item_type.code text _item_examples.case ; Scanning Transmission Electron Microscopy Mass Measurement-- PM28 isoforms solubilized in OTG were adsorbed for 1 min to glow discharged thin carbon films supported by a thick fenestrated carbon layer (directly after cation-exchange chromatography). The gold-plated copper grids were then washed on 8 drops of quartz double-distilled water and were freeze-dried at -80C overnight in the microscope. For mass analysis, annular dark-field images were recorded in a STEM (VG-HB5) at 80 kV and doses of 325 +/- 35 electrons/nm2. Digital acquisition of the images and microscope parameters, system calibration, and mass analysis were carried out as described previously. The total experimental error was calculated as the standard error of the mean, plus 5% of the measured particle mass to account for the absolute calibration uncertainty. ; save_ ##################### ## EM_VIRUS_ENTITY ## ##################### save_em_virus_entity _category.description ; Data items in the EM_VIRUS_ENTITY category record details of a virus component. ; _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' 'em_sample_description_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.entity_assembly_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.enveloped _em_virus_entity.empty 1 1 'VERTERBRATES' 'HOMO SAPIENS' 'VIRUS' 'STRAIN' '00.073.0.01.023' 'YES' 'NO' ; save_ save__em_virus_entity.id _item_description.description ; The value of _em_virus_entity.id must uniquely identify a set of the filament parameters for this assembly component. ; _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.entity_assembly_id _item_description.description ; The value of _em_virus_entity.entity_assembly_id identifies a particular assembly component. This data item is a pointer to _em_entity_assembly.id in the EM_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 _item_linked.child_name '_em_virus_entity.entity_assembly_id' _item_linked.parent_name '_em_entity_assembly.id' 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_enumeration.value 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_enumeration.value 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_examples.case 'STRAIN HIV-1' 'SEROTYPE A' 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. http://www.ncbi.nlm.nih.gov/ICTVdb/ ; _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.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_ ########################## ## EM_VIRUS_SHELLS ## ########################## save_em_virus_shells _category.description ; Data items in the EM_VIRUS_SHELLS category record details of the viral shell number, diameter of each shell and triangulation number of an icoshedral virus. ; _category.id em_virus_shells _category.mandatory_code no loop_ _category_key.name '_em_virus_shells.virus_entity_id' '_em_virus_shells.id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_sample_description_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_shells.virus_entity_id _em_virus_shells.id _em_virus_shells.shell_diameter _em_virus_shells.triangulation_num 1 1 400 4 ; save_ save__em_virus_shells.virus_entity_id _item_description.description ; The value of _em_virus_shells.virus_entity_id is a pointer to _em_virus_entity.id in the VIRUS_ENTITY category. ; _item.name '_em_virus_shells.virus_entity_id' _item.category_id em_virus_shells _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_virus_shells.virus_entity_id' _item_linked.parent_name '_em_virus_entity.id' save_ save__em_virus_shells.id _item_description.description ; The value of _em_em_virus_shells.id must uniquely identify the number and diameter of each virus protein shell and its triangulation number. ; _item.name '_em_virus_shells.id' _item.category_id em_virus_shells _item.mandatory_code yes _item_type.code code save_ save__em_virus_shells.shell_diameter _item_description.description ; The value of the diameter (in angstroms) for each protein shell of the virus. ; _item.name '_em_virus_shells.shell_diameter' _item.category_id em_virus_shells _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__em_virus_shells.triangulation_num _item_description.description ; The triangulation number (T number) refers to the organisation of the virus geometry. figure. It is given by the following relationship: T= h*2 + hk +k*2, where h and k are positive integers that define the position of the five-fold vertex on the original hexagonal net. ; _item.name '_em_virus_shells.triangulation_num' _item.category_id em_virus_shells _item.mandatory_code no _item_type.code int loop_ _item_examples.case 4 131 1 save_ ####################### # EM_HELICAL_ENTITY # ####################### save_em_helical_entity _category.description ; Data items in the EM_HELICAL_ENTITY category record details for a helical or filament type of assembly component. ; _category.id em_helical_entity _category.mandatory_code yes loop_ _category_key.name '_em_helical_entity.id' '_em_helical_entity.entity_assembly_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_sample_description_group' 'em_helical_group' save_ save__em_helical_entity.id _item_description.description ; The value of _em_helical_entity.id must uniquely identify a set of the filament parameters for this assembly component. ; _item.name '_em_helical_entity.id' _item.category_id em_helical_entity _item.mandatory_code yes _item_type.code code save_ save__em_helical_entity.entity_assembly_id _item_description.description ; The value of _em_helical_entity.entity_assembly_id identifies a particular assembly component. This data item is a pointer to _entity_assembly.id in the EM_ENTITY_ASSEMBLY category. ; _item.name '_em_helical_entity.entity_assembly_id' _item.category_id em_helical_entity _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_helical_entity.entity_assembly_id' _item_linked.parent_name '_em_entity_assembly.id' save_ save__em_helical_entity.details _item_description.description ; General details on the filaments studied ; _item.name '_em_helical_entity.details' _item.category_id em_helical_entity _item.mandatory_code no _item_type.code text save_ #save__em_helical_entity.delta_phi # _item_description.description #; The value for delta Phi to describe the repeat # parameters for a set of filaments #; # _item.name '_em_helical_entity.delta_phi' # _item.category_id em_helical_entity # _item.mandatory_code no # _item_type.code float # save_ #save__em_helical_entity.delta_z # _item_description.description #; The value for delta Z to describe the repeat # parameters for a set of filaments #; # _item.name '_em_helical_entity.delta_z' # _item.category_id em_helical_entity # _item.mandatory_code no # _item_type.code float # save_ save__em_helical_entity.dyad _item_description.description ; The value for the dyad to describe the repeat parameters for a set of filaments ; _item.name '_em_helical_entity.dyad' _item.category_id em_helical_entity _item.mandatory_code no _item_type.code line save_ save__em_helical_entity.axial_symmetry _item_description.description ; A description of the filament axial symmetry observed ; _item.name '_em_helical_entity.axial_symmetry' _item.category_id em_helical_entity _item.mandatory_code no _item_type.code text save_ #save__em_helical_entity.helical_family # _item_description.description #; The helical family of tubes used in the 3d reconstruction for # the helical assembly. The indices that characterise individual # helical families are determined by the numbers of the two # principal lines (helices) required to fill 360 degrees of azimuth. # Each family of tubes gives rise to a distinct # diffraction pattern determined by the number of principal 1,0 and # 0,1 helical lines around the tube circumference and by the # orientation of the surface lattice. Diffraction patterns from the # images of the helical tubes consist of closely spaced lines of # continuous intensity called layer-lines running perpendicular to # the tube axis. Within a helical family of tubes the layer-line # positions can also vary slightly, leading to a range of tube types # characterised by a particular helical selection rule. #; # _item.name '_em_helical_entity.helical_family' # _item.category_id em_helical_entity # _item.mandatory_code no # _item_type.code line # save_ #save__em_helical_entity.helical_pitch # _item_description.description #; The helical pitch of tubes used in the 3d reconstruction for # the helical assembly. #; # _item.name '_em_helical_entity.helical_pitch' # _item.category_id em_helical_entity # _item.mandatory_code no # _item_type.code line # save_ save__em_helical_entity.angular_rotation_per_subunit _item_description.description ; The angular rotation per helical subunit. ; _item.name '_em_helical_entity.angular_rotation_per_subunit' _item.category_id em_helical_entity _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__em_helical_entity.axial_rise_per_subunit _item_description.description ; The axial rise per subunit in the helical assembly. ; _item.name '_em_helical_entity.axial_rise_per_subunit' _item.category_id em_helical_entity _item.mandatory_code no _item_type.code float _item_units.code 'angstroms' save_ ########################## ## EM_2D_CRYSTAL_ENTITY ## ########################## save_em_2d_crystal_entity _category.description ; Data items in the EM_2D_CRYSTAL_ENTITY category record the symmetry details of a 2D crystal assembly component. ; _category.id em_2d_crystal_entity _category.mandatory_code no loop_ _category_key.name '_em_2d_crystal_entity.id' '_em_2d_crystal_entity.entity_assembly_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_sample_description_group' 'em_2D_crystal_group' save_ save__em_2d_crystal_entity.id _item_description.description ; The value of _em_2d_crystal_entity.id must uniquely identify a set of the crystal parameters for this assembly component. ; _item.name '_em_2d_crystal_entity.id' _item.category_id em_2d_crystal_entity _item.mandatory_code yes _item_type.code code save_ save__em_2d_crystal_entity.entity_assembly_id _item_description.description ; The value of _em_2d_crystal_entity.entity_assembly_id identifies an assembly component with 2d crystal symmetry. This data item is a pointer to _em_entity_assembly.id in the EM_ENTITY_ASSEMBLY category. ; _item.name '_em_2d_crystal_entity.entity_assembly_id' _item.category_id em_2d_crystal_entity _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_2d_crystal_entity.entity_assembly_id' _item_linked.parent_name '_em_entity_assembly.id' save_ save__em_2d_crystal_entity.length_a _item_description.description ; Unit-cell length a corresponding to the structure reported, in Angstroms. ; _item.name '_em_2d_crystal_entity.length_a' _item.category_id em_2d_crystal_entity _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__em_2d_crystal_entity.length_b _item_description.description ; Unit-cell length b corresponding to the structure reported, in Angstroms. ; _item.name '_em_2d_crystal_entity.length_b' _item.category_id em_2d_crystal_entity _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__em_2d_crystal_entity.angle_gamma _item_description.description ; Unit-cell angle gamma of the reported structure, in degrees. ; _item.name '_em_2d_crystal_entity.angle_gamma' _item.category_id em_2d_crystal_entity _item.mandatory_code no _item_default.value 90.0 loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__em_2d_crystal_entity.thickness _item_description.description ; The thickness of the crystal sample in the out-of-plane direction. ; _item.name '_em_2d_crystal_entity.thickness' _item.category_id em_2d_crystal_entity _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__em_2d_crystal_entity.space_group_name_H-M _item_description.description ; The 17 plane groups are classified as oblique, rectangular, square, and hexagonal. To describe 2D crystals of biological molecules, the plane groups are expanded to their equivalent noncentrosymmetric space groups. The space group setting is chosen such that the 2D crystal plane corresponds to the 'ab' plane of the space group. . Enumerated space group descriptions include the H-M plane group symbol and plane group class. ; _item.name '_em_2d_crystal_entity.space_group_name_H-M' _item.category_id em_2d_crystal_entity _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail 'P 1' 'p1, oblique' 'P 1 1 2' 'p2, oblique, 2-fold perpendicular to plane' 'P 1 2 1' 'pm, rectangular, 2-fold on b axis' 'P 1 21 1' 'pg, rectangular, 2(1)screw on b axis' 'C 1 2 1' 'cm, rectangular' 'P 2 2 2' '2mm, rectangular' 'P 21 2 2' 'p2mg, rectangular' 'P 21 21 2' 'p2gg, rectangular' 'C 2 2 2' 'c2mm, rectangular' 'P 4' 'p4, square' 'P 4 2 2' 'p4mm, square' 'P 4 21 2' 'p4gm, square' 'P 3' 'p3, hexagonal' 'P 3 1 2' 'p3m1, hexagonal' 'P 3 2 1' 'p31m, hexagonal' 'P 6' 'p6, hexagonal' 'P 6 2 2' 'p6mm, hexagonal' save_ save__em_2d_crystal_entity.Int_Tables_number _item_description.description ; Space-group number from International Tables for Crystallography, Vol. A (1987). ; _item.name '_em_2d_crystal_entity.Int_Tables_number' _item.category_id em_2d_crystal_entity _item.mandatory_code no _item_type.code int save_ save__em_2d_crystal_entity.details _item_description.description ; Additional details describing this 2D crystal component ; _item.name '_em_2d_crystal_entity.details' _item.category_id em_2d_crystal_entity _item.mandatory_code no _item_type.code text save_ ############################## # EM_SINGLE_PARTICLE_ENTITY # ############################## save_em_single_particle_entity _category.description ; Data items in the EM_SINGLE_PARTICLE_ENTITY category record details for a single particle assembly component. ; _category.id em_single_particle_entity _category.mandatory_code yes loop_ _category_key.name '_em_single_particle_entity.id' '_em_single_particle_entity.entity_assembly_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_sample_description_group' 'em_single_particle_group' save_ save__em_single_particle_entity.id _item_description.description ; The value of _em_single_particle_entity.id must uniquely identify a set of the single particle parameters for this assembly component. ; _item.name '_em_single_particle_entity.id' _item.category_id em_single_particle_entity _item.mandatory_code yes _item_type.code code save_ save__em_single_particle_entity.entity_assembly_id _item_description.description ; The value of _em_single_particle_entity.entity_assembly_id identifies a particular assembly component. This data item is a pointer to _em_entity_assembly.id in the EM_ENTITY_ASSEMBLY category. ; _item.name '_em_single_particle_entity.entity_assembly_id' _item.category_id em_single_particle_entity _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_single_particle_entity.entity_assembly_id' _item_linked.parent_name '_em_entity_assembly.id' save_ save__em_single_particle_entity.point_group_symmetry _item_description.description ; The point group symmetry of the single particle ; _item.name '_em_single_particle_entity.point_group_symmetry' _item.category_id em_single_particle_entity _item.mandatory_code no _item_type.code line save_ save__em_single_particle_entity.details _item_description.description ; Additional details describing the single particle ; _item.name '_em_single_particle_entity.details' _item.category_id em_single_particle_entity _item.mandatory_code no _item_type.code text save_ save__em_single_particle_entity.point_group_symmetry _item_description.description ; The point group symmetry of the single particle provided as the Schoenflies symbol. Descriptions for the Schoenflies symbols list the equivalent short Hermann-Mauguin symbols. For circular (Cn) and dihedral (Dn) point groups with n > 8, provide the value for n in related data item _em_single_particle_entity.point_group_symmetry_n. ; _item.name '_em_single_particle_entity.point_group_symmetry' _item.category_id em_single_particle_entity _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail C1 'asymmetric 1' C2 'circular 2' C3 'circular 3' C4 'circular 4' C5 'circular 5' C6 'circular 6' C7 'circular 7' C8 'circular 8' Cn 'circular n (n > 8)' D2 'dihedral 222' D3 'dihedral 32' D4 'dihedral 422' D5 'dihedral 52' D6 'dihedral 622' D7 'dihedral 72' D8 'dihedral 822' Dn 'dihedral n2 or n22 (n > 8)' T 'tetrahedral 23' O 'octahedral(cubic) 432' I 'icosahedral 235' save_ save__em_single_particle_entity.point_group_symmetry_n _item_description.description ; n value for circular and dihedral point group symmetries (n > 8). ; _item.name '_em_single_particle_entity.point_group_symmetry_n' _item.category_id em_single_particle_entity _item.mandatory_code no _item_type.code int _item_range.maximum . _item_range.minimum 8 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' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_biochemical_preparation_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.id 1 _em_sample_preparation.entity_assembly_id 1 _em_sample_preparation.pH 7.6 _em_sample_preparation.solution_id 1 _em_sample_preparation.sample_concentration 5 _em_sample_preparation.array_formation_id . _em_sample_preparation.support.id 1 ; save_ #save__em_sample_preparation.pdb_entry_id # _item_description.description #; This data item is a pointer to _entry.id in the ENTRY category. #; # _item.name '_em_sample_preparation.pdb_entry_id' # _item.category_id em_sample_preparation # _item.mandatory_code yes # _item_type.code code # _item_linked.child_name '_em_sample_preparation.pdb_entry_id' # _item_linked.parent_name '_entry.id' # save_ save__em_sample_preparation.entity_assembly_id _item_description.description ; This data item is a pointer to _entity_assembly.id in the entity_assembly category. ; _item.name '_em_sample_preparation.entity_assembly_id' _item.category_id em_sample_preparation _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_sample_preparation.entity_assembly_id' _item_linked.parent_name '_em_entity_assembly.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.details _item_description.description ; Details on the sample preparation ; _item.name '_em_sample_preparation.details' _item.category_id em_sample_preparation _item.mandatory_code yes _item_type.code text loop_ _item_examples.case _item_examples.detail 1 ; Selectively stained by injection of horseradish peroxidase, embedded in Spurr's resin and cut into 2-3 um thick sections. ; 2 ; Enzyme Preparations. S. cerevisiae PDC was purified to near homogeneity from baker's yeast by modification of a published procedure. Highly purified E1 was obtained by resolution of PDC with 2 M NaCl at pH 7.3 followed by FPLC on a Superdex 200 column. The weight-average molecular weight of the PDC was determined by light scattering measurement to be ~8 x 106. On the basis of the known molecular weight of the complex and its component enzymes and the experimentally determined polypeptide chain ratios of E2/BP/E3, we estimated that the subunit composition of the S. cerevisiae PDC is ~24 E1 tetramers, 60 E2 monomers, 12 BP monomers, and 8 E3 dimers. Sufficient E1 was added to a sample of the PDC preparation to increase the molar ratio of E1/E2 core to 60:1. This product is designated larger PDC or ~60 E1/E2 core PDC ; 3 ; embedment in vitreous ice. ; 4 ; Detergent-solubilized particles eluted from the cation-exchange column were directly adsorbed for 1 min to parlodion carbon-coated copper grids rendered hydrophilic by glow discharge at low pressure in air. Grids were washed with 4 drops of double-distilled water and stained with 2 drops of 0.75% uranyl formate. Images were recorded on Eastman Kodak Co. SO-163 sheet film with a Hitachi H-7000 electron microscope operated at 100 kV. Electron micrographs of single particles adsorbed to the carbon film were digitized using a Leafscan-45 scanner (Leaf Systems, Inc., Westborough, MA). ; 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 yes _item_type.code float save_ save__em_sample_preparation.solution_id _item_description.description ; This data item is a pointer to _em_solution_composition.id in the EM_SOLUTION_COMPOSITION category. ; _item.name '_em_sample_preparation.solution_id' _item.category_id em_sample_preparation _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_sample_preparation.solution_id' _item_linked.parent_name '_em_solution_composition.id' 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 yes _item_type.code float _item_units.code mg_per_ml save_ save__em_sample_preparation.array_formation_id _item_description.description ; This data item is a pointer to _em_array_formation.id in the ARRAY_FORMATION category. ; _item.name '_em_sample_preparation.array_formation_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 _item_linked.child_name '_em_sample_preparation.support_id' _item_linked.parent_name '_em_sample_support.id' 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' 'em_biochemical_preparation_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 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' QUANTAFOIL OTHER 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 MESH 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 loop_ _item_examples.case _item_examples.detail 1 'This grid plus sample was kept at -170 deg C for a month before use' 2 ; A 3-microliter sample of each PDC preparation (~0.35 mg/ml containing 20 microgram/ml bacitracin) was deposited, blotted, and quick-frozen in liquid ethane on a glow-discharged carbon-coated holey grid. The vitrified samples were recorded at ~1 micrometer under focus at ~10 e/Angstroms-squared dose for image processing. A second exposure of ~2-3 micrometer under focus was recorded and used as an aid in analyzing the images with the focal pair method. The images were recorded on Kodak SO 163 film at a nominal magnification of x50,000 in a JEOL JEM 1200 electron microscope operated at 100 kV. ; 3 ; Orientation of 4300 Ribosome projections identified by 3D projection matching using low resolution reference. (Penczek et al., 1994). Reconstruction (SIRT) simultaneously performed CTF correction (Zhu et al. submitted). ; 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_ARRAY_FORMATION ## ######################## save_em_array_formation _category.description ; Data items in the EM_ARRAY_FORMATION category record details of growth conditions for the array samples. ; _category.id em_array_formation _category.mandatory_code no loop_ _category_key.name '_em_array_formation.id' '_em_array_formation.type' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_biochemical_preparation_group' 'em_2D_crystal_group' 'em_helical_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_array_formation.id 1 _em_array_formation.type "2D-CRYSTAL" _em_array_formation.method . _em_array_formation.apparatus . _em_array_formation.atmosphere 'room air' _em_array_formation.pH 5.2 _em_array_formation.temp 18 _em_array_formation.time . _em_array_formation.buffer_id 2 _em_array_formation.details 'on grid' _em_array_formation.citation_id 2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__em_array_formation.id _item_description.description ; The value of _em_array_formation.id must uniquely identify the sample. ; _item.name '_em_array_formation.id' _item.category_id em_array_formation _item.mandatory_code yes _item_type.code code save_ save__em_array_formation.type _item_description.description ; The value of _em_array_formation.type must identifies the type of array studied. ; _item.name '_em_array_formation.type' _item.category_id em_array_formation _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value 'TUBE' '2D-CRYSTAL' '3D-CRYSTAL' 'ICOSAHEDRON' # '2D-ARRAY' # '3D-ARRAY' 'OTHER' save_ save__em_array_formation.method _item_description.description ; The method used for growing the array. ; _item.name '_em_array_formation.method' _item.category_id em_array_formation _item.mandatory_code no _item_type.code line _item_examples.case 'lipid monolayer' save_ save__em_array_formation.apparatus _item_description.description ; The type of the apparatus used for growing the array. ; _item.name '_em_array_formation.apparatus' _item.category_id em_array_formation _item.mandatory_code no _item_type.code line _item_examples.case 'Langmuir trough' save_ save__em_array_formation.atmosphere _item_description.description ; The type of atmosphere in which arrays were grown. ; _item.name '_em_array_formation.atmosphere' _item.category_id em_array_formation _item.mandatory_code no _item_type.code line _item_examples.case 'room air' save_ save__em_array_formation.pH _item_description.description ; the pH value used for growing the array. ; _item.name '_em_array_formation.pH' _item.category_id em_array_formation _item.mandatory_code no _item_type.code float _item_examples.case 4.7 save_ save__em_array_formation.temp _item_description.description ; The value of the temperature in degrees Kelvin used for growing the arrays. ; _item.name '_em_array_formation.temp' _item.category_id em_array_formation _item.mandatory_code no _item_type.code float _item_units.code kelvins _item_examples.case 293 save_ save__em_array_formation.time _item_description.description ; The length of time required to grow the array. ; _item.name '_em_array_formation.time' _item.category_id em_array_formation _item.mandatory_code no _item_type.code line _item_examples.case 'approximately 2 days' save_ save__em_array_formation.solution_id _item_description.description ; This data item is a pointer to _em_solution_composition.id in the EM_SOLUTION_COMPOSITION category. ; _item.name '_em_array_formation.solution_id' _item.category_id em_array_formation _item.mandatory_code no _item_type.code code save_ save__em_array_formation.details _item_description.description ; Any additional items concerning array growth. ; _item.name '_em_array_formation.details' _item.category_id em_array_formation _item.mandatory_code no _item_type.code text _item_examples.case ; Two-dimensional Crystallization-- Purified protein (2 mg/ml) was mixed with E. coli lipids solubilized in OTG (mixed micelles stock solution, 4 mg/ml E. coli lipids in 20 mM Mes-NaOH (pH 6), 5% OTG, 0.01% NaN3) to achieve a lipid to protein ratio of 1 (w/w). The final protein concentration was adjusted to 1.33 mg/ml, and the final OTG content was adjusted to 1.93%. The reconstitution mixture (60 microliters) was preincubated at room temperature for 30 min and dialyzed against 1.5 liters of 10 mM Mes-NaOH (pH 6), 100 mM NaCl, 100 mM MgCl2, 2 mM dithiothreitol, 0.01% NaN3 for 24 h at room temperature, 24 h at 37 C, and another 24 h at room temperature. ; save_ #save__em_array_formation.number_2d_crystals # _item_description.description #; The number of 2d crystals imaged. #; # _item.name '_em_array_formation.number_2d_crystals' # _item.category_id em_array_formation # _item.mandatory_code no # _item_type.code int # save_ #save__em_array_formation.mean_2d_crystal_size # _item_description.description #; The approximate size (microns squared) of 2d crystals imaged. #; # _item.name '_em_array_formation.mean_2d_crystal_size' # _item.category_id em_array_formation # _item.mandatory_code no # _item_type.code float # _item_units.code microns_squared # save_ # save__em_array_formation.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_array_formation.citation_id' _item.category_id em_array_formation _item.mandatory_code no _item_linked.child_name '_em_array_formation.citation_id' _item_linked.parent_name '_citation.id' _item_type.code code save_ save__em_array_formation.buffer_id _item_description.description ; This data item is a pointer to _em_solution_composition.id. ; _item.name '_em_array_formation.buffer_id' _item.category_id em_array_formation _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_array_formation.buffer_id' _item_linked.parent_name '_em_solution_composition.id' save_ ############################# ## EM_SOLUTION_COMPOSITION ## ############################# save_em_solution_composition _category.description ; Data items in the EM_SOLUTION_COMPOSITION category record details of the sample buffer. ; _category.id em_solution_composition _category.mandatory_code no _category_key.name '_em_solution_composition.id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_biochemical_preparation_group' save_ save__em_solution_composition.id _item_description.description ; The value of _em_solution_composition.id must uniquely identify the sample solution conditions. ; _item.name '_em_solution_composition.id' _item.category_id em_solution_composition _item.mandatory_code yes _item_type.code code save_ save__em_solution_composition.name _item_description.description ; The name of the buffer. ; _item.name '_em_solution_composition.name' _item.category_id em_solution_composition _item.mandatory_code no _item_type.code line _item_examples.case 'Acetic acid' save_ save__em_solution_composition.pH _item_description.description ; The pH of the buffer. ; _item.name '_em_solution_composition.pH' _item.category_id em_solution_composition _item.mandatory_code no _item_type.code float _item_examples.case 6.93 save_ save__em_solution_composition.details _item_description.description ; Any additional details to do with buffer. ; _item.name '_em_solution_composition.details' _item.category_id em_solution_composition _item.mandatory_code no _item_type.code text _item_examples.case 'aerated' 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' 'em_specimen_preparation_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.protocol "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 loop_ _item_enumeration.value 'REICHERT PLUNGER' LEICA GATAN VITROBOT HOME-MADE save_ save__em_vitrification.protocol _item_description.description ; The procedure for vitrification. ; _item.name '_em_vitrification.protocol' _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' 'em_data_collection_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_id 1 _em_imaging.specimen_holder_model 'gatan 626-0300' _em_imaging.details . _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_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.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 _item_linked.child_name '_em_imaging.detector_id' _item_linked.parent_name '_em_detector.id' save_ save__em_imaging.image_scanning_id _item_description.description ; The value of _em_imaging.image_scans_id identifies the scanning protocol used in the experiment. The item is a pointer to _em_image_scanning.id in category EM_IMAGE_SCANNING. ; _item.name '_em_imaging.image_scanning_id' _item.category_id em_imaging _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_imaging.image_scanning_id' _item_linked.parent_name '_em_image_scanning.id' save_ save__em_imaging.microscope_id _item_description.description ; A pointer to _em_microscope.id in the EM_MICROSCOPE category ; _item.name '_em_imaging.microscope_id' _item.category_id em_imaging _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_imaging.microscope_id' _item_linked.parent_name '_em_microscope.id' 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 _item_linked.child_name '_em_imaging.sample_support_id' _item_linked.parent_name '_em_sample_support.id' 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_enumeration.value 'BRIGHT FIELD' 'DARK FIELD' DIFFRACTION OTHER 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 yes _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_enumeration.value 'FLOOD BEAM' 'SPOT SCAN' OTHER save_ save__em_imaging.condenser_aperture_details _item_description.description ; The details about the condenser aperture used including dimension, material, and treatment. ; _item.name '_em_imaging.condenser_aperture_details' _item.category_id em_imaging _item.mandatory_code no _item_type.code text save_ save__em_imaging.spot_size _item_description.description ; Description of the spot size as determined by the setting of the first condenser lens. ; _item.name '_em_imaging.spot_size' _item.category_id em_imaging _item.mandatory_code no _item_type.code text 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 yes _item_type.code line loop_ _item_enumeration.value 'GATAN HELIUM' 'GATAN LIQUID NITROGEN' 'GATAN CT3500 CRYO-TRANSFER' 'GATAN CT3500TR TILT-ROTATE CRYO-TRANSFER' 'GATAN 626 CRYO-TRANSFER' 'GATAN 630 HIGH TILT TOMOGRAPHY' 'GATAN 910 MULTISPECIMEN HOLDER' 'GATAN 915 DOUBLE TILT HOLDER' 'GATAN SINGLE TILT ULTRA HIGH RESOLUTION NITROGEN COOLING HOLDER, UHRST 3500' 'GATAN DOUBLE TILT HIGH RESOLUTION NITROGEN COOLING HOLDER, CHDT 3504' 'GATAN SINGLE TILT HEATING / NITROGEN COOLING HOLDER, HC 3500' 'GATAN SINGLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER, HCHST 3008' 'GATAN ULTRA LOW TEMPERATURE SINGLE TILT HELIUM COOLING HOLDER, ULTST' 'GATAN DOUBLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER, HCHDT 3010' 'GATAN ULTRA LOW TEMPERATURE DOUBLE TILT HELIUM COOLING HOLDER, ULTDT' 'GATAN 677 FIB MULTIPLE SPECIMEN HOLDER' 'GATAN 912J HIGH TILT TOMOGRAPHY HOLDER FOR URP POLE PIECES' 'GATAN 912P HIGH TILT TOMOGRAPHY HOLDER FOR ULTRA-TWIN POLE PIECES' 'GATAN 914 NITROGEN COOLED CRYOTRANSFER TOMOGRAPHY HOLDER' 'GATAN 916 ROOM TEMPERATURE TOMOGRAPHY HOLDER' 'OXFORD CT3500P' 'FISCHIONE 2020 TOMOGRAPHY HOLDER' 'JEOL SPECIFIC' 'FEI SPECIFIC' 'HITACHI SPECIFIC' 'ZEISS SPECIFIC' OTHER 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.imaging_cryogen _item_description.description ; The imaging cryogen used ; _item.name '_em_imaging.imaging_cryogen' _item.category_id em_imaging _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value Helium Nitrogen OTHER 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.electron_dose_range _item_description.description ; The electron dose range received by the specimen (electrons per square angstrom). ; _item.name '_em_imaging.electron_dose_range' _item.category_id em_imaging _item.mandatory_code no _item_type.code line _item_examples.case '0.9 - 1.1' # _item_related.related_name '_em_imaging.electron_dose' # _item_related.function_code alternate_exclusive save_ save__em_imaging.electron_dose_method _item_description.description ; The method used to determine the electron dose received by the specimen. ; _item.name '_em_imaging.electron_dose_method' _item.category_id em_imaging _item.mandatory_code no _item_type.code text 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.objective_aperture_details _item_description.description ; Description of the objective aperture used including the dimension, material, and treatment. ; _item.name '_em_imaging.objective_aperture_details' _item.category_id em_imaging _item.mandatory_code no _item_type.code text save_ save__em_imaging.selective_aperture _item_description.description ; Description of the selective aperture used ; _item.name '_em_imaging.selective_aperture' _item.category_id em_imaging _item.mandatory_code no _item_type.code text save_ save__em_imaging.diffraction_camera_length _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.diffraction_camera_length' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code millimetres 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.calibrated_magnification_method _item_description.description ; The method used to determine the calibrated magnification. ; _item.name '_em_imaging.calibrated_magnification_method' _item.category_id em_imaging _item.mandatory_code no _item_type.code text 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' loop_ _item_enumeration.value 'FEI' 'JEOL OMEGA' 'GATAN GIF' 'GATAN TRIDIEM' 'ZEISS OMEGA' 'ZEISS MANDOLINEN' 'GATAN ENFINA' save_ ### --?? Enumerated list with other (post column, in column) 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.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_ # 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 loop_ _item_examples.case _item_examples.detail 1 ; Tilt series for tomographic reconstruction was recorded ove