########################################################################### # # File: mmcif_em.dic # Date: Mon Aug 16 07:18:26 EDT 2021 # # 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 # mmcif_em-def-ilg.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. This dictionary incorporates the recommendations of a 2004 Cryo-EM Workshop - http://rcsb-cryo-em-development.rutgers.edu/workshop/participant.html. The content of this dictionary has largely been incorporated into the wwPDB Exchange Dictionary. Further development of 3DEM data definitions has been done within the wwPDB dictionary. ; _dictionary.title mmcif_em.dic _dictionary.datablock_id mmcif_em.dic _dictionary.version 0.015 # 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 ; 0.015 2013-1018 ; Changes (jdw): + Dictionary description updated. ; ### 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 over a 124 degree angular range, using a 2 degree angular interval, with a high voltage electron microscope. Acceleration voltage = 1.0 MV. Em = AEI. Alignment using gold markers and cross-correlation. Reconstruction technique: Modified back-projection. Direction of missing wedge: ; 2 ; All image processing steps described below were performed using the Semper image processing system(Synoptics Ltd., Cambridge, United Kingdom). ; save_ ################# ## EM_DETECTOR ## ################# save_em_detector _category.description ; Data items in the EM_DETECTOR category record details of the image detector type. ; _category.id em_detector _category.mandatory_code no loop_ _category_key.name '_em_detector.entry_id' '_em_detector.id' loop_ _category_group.id 'inclusive_group' 'em_group' '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_detector.entry_id 1DYL _em_detector.id 1 _em_detector.type 'FILM' ; save_ save__em_detector.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_detector.entry_id' _item.category_id em_detector _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_detector.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_detector.id _item_description.description ; The value of _em_detector.id must uniquely identify the detector used for imaging. ; _item.name '_em_detector.id' _item.category_id em_detector _item.mandatory_code yes _item_type.code code save_ save__em_detector.type _item_description.description ; The detector type used for recording images. Usually film or CCD camera. ; _item.name '_em_detector.type' _item.category_id em_detector _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value 'FILM' 'CCD' 'OTHER' save_ ###################### ## EM_DETECTOR_FILM ## ###################### save_em_detector_film _category.description ; Data items in the EM_DETECTOR_FILM category record details of the image detector type. ; _category.id em_detector_film _category.mandatory_code no _category_key.name '_em_detector_film.detector_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_detector_film.entry_id 1DYL _em_detector_film.id 1 _em_detector_film.details . _em_detector_film.type 'KODAK SO163 FILM' ; save_ save__em_detector_film.detector_id _item_description.description ; The value of _em_detector_film.detector_id must uniquely identify the characteristics of the film detector. The value of _em_detector_film.detector_id is a pointer to _em_detector.id in category EM_DETECTOR. ; _item.name '_em_detector_film.detector_id' _item.category_id em_detector_film _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_detector_film.detector_id' _item_linked.parent_name '_em_detector.id' save_ save__em_detector_film.details _item_description.description ; Any additional information about the detection system. ; _item.name '_em_detector_film.details' _item.category_id em_detector_film _item.mandatory_code no _item_type.code text save_ save__em_detector_film.film_type _item_description.description ; The film type used for recording images. ; _item.name '_em_detector_film.film_type' _item.category_id em_detector_film _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value 'KODAK SO163' 'ILFORD ELECTRON MICROSCOPE FILM' 'FUJI FG' 'FUJI IP' 'KODAK 4489' 'AGFA SCIENTIA FILM 23D56' 'OTHER' save_ #save__em_detector_film.pixel_size # _item_description.description #; The detector pixel size #; # _item.name '_em_detector_film.pixel_size' # _item.category_id em_detector_film # _item.mandatory_code no # _item_type.code line # save_ save__em_detector_film.film_processing_conditions _item_description.description ; Description of film_processing_conditions ; _item.name '_em_detector_film.film_processing_conditions' _item.category_id em_detector_film _item.mandatory_code no _item_type.code text save_ save__em_detector_film.dimension_x _item_description.description ; The detector dimension in x ; _item.name '_em_detector_film.dimension_x' _item.category_id em_detector_film _item.mandatory_code no _item_type.code int save_ save__em_detector_film.dimension_y _item_description.description ; The detector dimension in y ; _item.name '_em_detector_film.dimension_y' _item.category_id em_detector_film _item.mandatory_code no _item_type.code int save_ ##################### ## EM_DETECTOR_CCD ## ##################### save_em_detector_CCD _category.description ; Data items in the EM_DETECTOR_CCD category record details of the CCD detector type. ; _category.id em_detector_CCD _category.mandatory_code no _category_key.name '_em_detector_CCD.detector_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_data_collection_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - ; ; _em_detector_CCD.detector_id 1 _em_detector_CCD.details . _em_detector_CCD.type 'PROSCAN' ; save_ save__em_detector_CCD.detector_id _item_description.description ; The value of _em_detector_CCD.detector_id must uniquely identify the description of the CCD detector. The value of _em_detector_CCD.detector_id is a pointer to _em_detector.id in category EM_DETECTOR. ; _item.name '_em_detector_CCD.detector_id' _item.category_id em_detector_CCD _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_detector_CCD.detector_id' _item_linked.parent_name '_em_detector.id' save_ save__em_detector_CCD.details _item_description.description ; Any additional information about the detection system. ; _item.name '_em_detector_CCD.details' _item.category_id em_detector_CCD _item.mandatory_code no _item_type.code text save_ save__em_detector_CCD.model _item_description.description ; The CCD detector model used for recording images. ; _item.name '_em_detector_CCD.model' _item.category_id em_detector_CCD _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value AMT 'GATAN 673' 'GATAN 676' 'GATAN 692' 'GATAN 1000' 'GATAN 4000' 'GATAN ES500W' 'GATAN ES300' 'GATAN MSC 600W (MODEL 792)' 'GATAN MSC 600CW (MODEL 791)' 'GATAN MSC 600HP (MODEL 794)' 'GATAN USC 4000 (MODEL 895)' 'GATAN USC 4000SP (MODEL 890)' 'GATAN USC 1000 (MODEL 894)' PROSCAN 'TVIPS BIOCAM' 'TVIPS TEMCAM F214' 'TVIPS TEMCAM F224' 'TVIPS FASTSCAN F114' 'TVIPS F114 - ON-AXIS' 'TVIPS F114FX - OFF-AXIS' 'TVIPS F114NX - NEAR-AXIS' 'TVIPS F114R - RETRACTABLE' 'TVIPS F214 - 2K RESOLUTION, 14 MICROMETER PIXEL SIZE, 12 BIT' 'TVIPS F224HD - 2K RESOLUTION, 24 MICROMETER PIXEL SIZE, 16 BIT' 'TVIPS F415/MP - 4K RESOLUTION, 15 MICROMETER PIXEL SIZE, 16 BIT' 'OTHER' save_ save__em_detector_CCD.pixel_size _item_description.description ; The detector pixel size ; _item.name '_em_detector_CCD.pixel_size' _item.category_id em_detector_CCD _item.mandatory_code no _item_type.code line save_ save__em_detector_CCD.dimension_x _item_description.description ; The detector dimension in x ; _item.name '_em_detector_CCD.dimension_x' _item.category_id em_detector_CCD _item.mandatory_code no _item_type.code int save_ save__em_detector_CCD.dimension_y _item_description.description ; The detector dimension in y ; _item.name '_em_detector_CCD.dimension_y' _item.category_id em_detector_CCD _item.mandatory_code no _item_type.code int save_ ####################### ## EM_IMAGE_SCANNING ## ####################### save_em_image_scanning _category.description ; Data items in the EM_IMAGE_SCANNING category record type of image scanning device used digitized the image. ; _category.id em_image_scanning _category.mandatory_code no loop_ _category_key.name '_em_image_scanning.entry_id' '_em_image_scanning.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_image_scanning.entry_id 1DYL _em_image_scanning.id 2 _em_image_scanning.type 'FILM_SCANNING' ; save_ save__em_image_scanning.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_image_scanning.entry_id' _item.category_id em_image_scanning _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_image_scanning.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_image_scanning.id _item_description.description ; The value of _em_image_scanning.id must uniquely identify a particular scanning protocol. ; _item.name '_em_image_scanning.id' _item.category_id em_image_scanning _item.mandatory_code yes _item_type.code code save_ save__em_image_scanning.type _item_description.description ; The type of scanning used in the experiment. ; _item.name '_em_image_scanning.type' _item.category_id em_image_scanning _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value 'FILM SCANNING' 'CCD READOUT' 'OTHER' save_ save__em_image_scanning.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_image_scanning.citation_id' _item.category_id em_image_scanning _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_image_scanning.citation_id' _item_linked.parent_name '_citation.id' save_ ############################ ## EM_IMAGE_SCANNING_FILM ## ############################ save_em_image_scanning_film _category.description ; Data items in the EM_IMAGE_SCANNING_FILM category record details of the film scanning device (microdensitometer) and parameters for digitization of the image. ; _category.id em_image_scanning_film _category.mandatory_code no loop_ _category_key.name '_em_image_scanning_film.image_scanning_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_image_scanning_film.image_scanning_id 2 _em_image_scanning_film.details . _em_image_scanning_film.scanner_model . _em_image_scanning_film.step_size . _em_image_scanning_film.od_range . _em_image_scanning_film.bits_per_pixel . ; save_ save__em_image_scanning_film.image_scanning_id _item_description.description ; The value of _em_image_scanning_film.id must uniquely identify a set of image scanning parameters. This value is a pointer to '_em_image_scanning_film.id' in the EM_IMAGE_SCANNING category. ; _item.name '_em_image_scanning_film.image_scanning_id' _item.category_id em_image_scanning_film _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_image_scanning_film.image_scanning_id' _item_linked.parent_name '_em_image_scanning.id' save_ save__em_image_scanning_film.details _item_description.description ; Any additional details about scanning film images. ; _item.name '_em_image_scanning_film.details' _item.category_id em_image_scanning_film _item.mandatory_code no _item_type.code text save_ save__em_image_scanning_film.scanner_model _item_description.description ; The film scanner model. ; _item.name '_em_image_scanning_film.scanner_model' _item.category_id em_image_scanning_film _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value 'ZEISS SCAI' 'EMIL 10' OPTRONICS 'PERKIN ELMER' TEMSCAN NIKON 'NIKON SUPERCOOLSCAN 8000' 'NIKON SUPERCOOLSCAN 9000' 'JOYCE LOEBL' 'HEIDELBERG TANGO' OTHER save_ save__em_image_scanning_film.step_size _item_description.description ; The sampling step size (microns) set on the scanner. ; _item.name '_em_image_scanning_film.step_size' _item.category_id em_image_scanning_film _item.mandatory_code no _item_type.code float _item_units.code microns save_ save__em_image_scanning_film.od_range _item_description.description ; The optical density range (OD=-log 10 transmission). To the eye OD=1 appears light grey and OD=3 is opaque. ; _item.name '_em_image_scanning_film.od_range' _item.category_id em_image_scanning_film _item.mandatory_code no _item_type.code float _item_examples.case 1.4 save_ save__em_image_scanning_film.bits_per_pixel _item_description.description ; The number of bits per pixel used in digitization. ; _item.name '_em_image_scanning_film.bits_per_pixel' _item.category_id em_image_scanning_film _item.mandatory_code no _item_type.code int _item_examples.case 8 save_ save__em_image_scanning_film.spot_size _item_description.description ; The spot size ; _item.name '_em_image_scanning_film.spot_size' _item.category_id em_image_scanning_film _item.mandatory_code no _item_type.code text save_ save__em_image_scanning_film.binning_x _item_description.description ; The detector binning in x direction ; _item.name '_em_image_scanning_film.binning_x' _item.category_id em_image_scanning_film _item.mandatory_code no _item_type.code int save_ save__em_image_scanning_film.binning_y _item_description.description ; The detector binning in y direction ; _item.name '_em_image_scanning_film.binning_y' _item.category_id em_image_scanning_film _item.mandatory_code no _item_type.code int save_ ########################### ## EM_IMAGE_READOUT_CCD ## ########################### save_em_image_readout_ccd _category.description ; Data items in the EM_IMAGE_READOUT_CCD category record details of the CCD readout and parameters for digitization of the image. ; _category.id em_image_readout_ccd _category.mandatory_code no loop_ _category_key.name '_em_image_readout_ccd.image_scanning_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_data_collection_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - ; ; _em_image_readout_ccd.image_scanning_id 2 _em_image_readout_ccd.details . ; save_ save__em_image_readout_ccd.image_scanning_id _item_description.description ; The value of _em_image_readout_ccd.id must uniquely identify a set of CCD image scanning parameters. This value is a pointer to '_em_image_readout_ccd.id' in the EM_IMAGE_SCANNING category. ; _item.name '_em_image_readout_ccd.image_scanning_id' _item.category_id em_image_readout_ccd _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_image_readout_ccd.image_scanning_id' _item_linked.parent_name '_em_image_scanning.id' save_ save__em_image_readout_ccd.details _item_description.description ; Any additional details about CCD image scanning. ; _item.name '_em_image_readout_ccd.details' _item.category_id em_image_readout_ccd _item.mandatory_code no _item_type.code text save_ save__em_image_readout_ccd.binning_x _item_description.description ; The detector binning in x direction ; _item.name '_em_image_readout_ccd.binning_x' _item.category_id em_image_readout_ccd _item.mandatory_code no _item_type.code int save_ save__em_image_readout_ccd.binning_y _item_description.description ; The detector binning in y direction ; _item.name '_em_image_readout_ccd.binning_y' _item.category_id em_image_readout_ccd _item.mandatory_code no _item_type.code int save_ save__em_image_readout_ccd.offset_x _item_description.description ; The detector offset in x from the top left corner of the CCD ; _item.name '_em_image_readout_ccd.offset_x' _item.category_id em_image_readout_ccd _item.mandatory_code no _item_type.code int save_ save__em_image_readout_ccd.offset_y _item_description.description ; The detector offset in y from the top left corner of the CCD ; _item.name '_em_image_readout_ccd.offset_y' _item.category_id em_image_readout_ccd _item.mandatory_code no _item_type.code int save_ save__em_image_readout_ccd.speed _item_description.description ; The detector read-out speed ; _item.name '_em_image_readout_ccd.speed' _item.category_id em_image_readout_ccd _item.mandatory_code no _item_type.code int save_ ############################ ## EM_PARTICLE_SELECTION ## ############################ save_em_particle_selection _category.description ; Data items in the EM_PARTICLE_SELECTION category record details about the method to pick select from the raw micrographs. ; _category.id em_particle_selection _category.mandatory_code no loop_ _category_key.name '_em_particle_selection.id' '_em_particle_selection.entity_assembly_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_image_selection_group' 'em_single_particle_group' save_ save__em_particle_selection.id _item_description.description ; The value of _em_particle_selection.id uniquely identifies a set of selection conditions for this entity. ; _item.name '_em_particle_selection.id' _item.category_id em_particle_selection _item.mandatory_code yes _item_type.code code save_ save__em_particle_selection.entity_assembly_id _item_description.description ; The value of _em_particle_selection.entity_assembly_id identifies assembly or assembly component associated with this set of selection conditions. This data item is a pointer to _em_entity_assembly.id in the EM_ENTITY_ASSEMBLY category. ; _item.name '_em_particle_selection.entity_assembly_id' _item.category_id em_particle_selection _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_particle_selection.entity_assembly_id' _item_linked.parent_name '_em_entity_assembly.id' save_ save__em_particle_selection.pre_processing_filters_details _item_description.description ; Description of the pre-processing filters used ; _item.name '_em_particle_selection.pre_processing_filters_details' _item.category_id em_particle_selection _item.mandatory_code yes _item_type.code text save_ save__em_particle_selection.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_particle_selection.citation_id' _item.category_id em_particle_selection _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_particle_selection.citation_id' _item_linked.parent_name '_citation.id' save_ save__em_particle_selection.correlation_threshold _item_description.description ; Maxima having correlation scores below this threshold are not considered as possible particle locations. ; _item.name '_em_particle_selection.correlation_threshold' _item.category_id em_particle_selection _item.mandatory_code yes _item_type.code float save_ save__em_particle_selection.local_maxima_radius _item_description.description ; Radius used to test if a point's correlation score is locally maximal. ; _item.name '_em_particle_selection.local_maxima_radius' _item.category_id em_particle_selection _item.mandatory_code yes _item_type.code float save_ save__em_particle_selection.grow_threshold _item_description.description ; Minimum difference between a peak and its surrounding trough in the correlation score. ; _item.name '_em_particle_selection.grow_threshold' _item.category_id em_particle_selection _item.mandatory_code yes _item_type.code float save_ save__em_particle_selection.min_radius _item_description.description ; Minimum radius of the peaks in the correlation score. ; _item.name '_em_particle_selection.min_radius' _item.category_id em_particle_selection _item.mandatory_code yes _item_type.code float save_ save__em_particle_selection.max_radius _item_description.description ; Maximium radius of the peaks in the correlation score. ; _item.name '_em_particle_selection.max_radius' _item.category_id em_particle_selection _item.mandatory_code yes _item_type.code float save_ save__em_particle_selection.details _item_description.description ; General details on the particle picking method ; _item.name '_em_particle_selection.details' _item.category_id em_particle_selection _item.mandatory_code yes _item_type.code text loop_ _item_examples.case _item_examples.detail 1 ; Particles were picked using a program written in-house for selecting filaments. Lines are drawn over the filaments using the computer mouse, and the program selects coordinates for boxing the particles at a user-selected interval while keeping track of groups of particles coming from the same filament. This is useful where polarity can be determined per filament by two-dimensional averaging. The program also keeps track of the angle of the overlaid, user-drawn line, which is used for preliminary vertical orientation of the particles. 8440 particles of 80 x 80 pixel size were selected from the filaments. ; 2 ; A reference was established by selecting a well preserved particle and symmetrizing it 20-fold rotationally. Cross-correlation functions of this reference with images of digitized micrographs containing adsorbed particles of PM28 revealed correlation peaks at the particle positions, irrespective of their angular orientation. Using this particle picking method a gallery of 4096 particles was created. ; save_ save__em_particle_selection.method _item_description.description ; The particle picking method ; _item.name '_em_particle_selection.method' _item.category_id em_particle_selection _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail 'Template-based' . 'Edge detection-based' . 'Intensity comparison' . 'Texture-based' . 'Neural network' . 'Learning based' . 'Manually selected' . Hybrid . 'Lata method' ; Ultramicroscopy 58 (1995) 381-391 particles are automatically classified according to texture descriptors. ; 'Local Fast Correlation' ; B.K. Rath and J. Frank, Journal of Structural Biology, Volume 145, Issues 1-2, January 2004, Pages 84-90 and Alan Roseman (Ultramicroscopy, Vol 94, Issues 3-4, (2003), 225-236) ; save_ save__em_particle_selection.centering_method _item_description.description ; The particle picking centering method The so-called center of gravity method where the image is scanned and the intensity peaks calculated to find the center of the particle 'mass'. The image is then shifted by the correct amounts to maximize the number of peaks near the center. Another centering method averages all the picked particles together, and then cross correlates each individual particle to the average. The cross correlation function is used to determine by how much to shift each particle when trying to center it. When all the particles have been cross correlated to the average and shifted, a new average is generated. Once again, all the particles are compared to the new average, and shifted as necessary to center them as best as possible. This iterative process is repeated until no significant shift is necessary for all the particles Crosscorrelating to a global average is but one variation on this theme. Similar methods also use an external model or a rotational average of the particle itself as the centering reference. Unfortunately, it can be difficult to obtain a reasonable external refernce, so a global average or a rotational average are most often used. ; _item.name '_em_particle_selection.centering_method' _item.category_id em_particle_selection _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value 'centre of gravity' 'cross correlation' save_ ################################## ## EM_SINGLE_PARTICLE_SELECTION ## ################################## save_em_single_particle_selection _category.description ; Data items in the EM_SINGLE_PARTICLE_SELECTION category record details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs. ; _category.id em_single_particle_selection _category.mandatory_code no _category_key.name '_em_single_particle_selection.selection_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_image_selection_group' 'em_single_particle_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_single_particle_selection.selection_id 1 _em_single_particle_selection.number_particles 5267 _em_single_particle_selection.software_name 1 _em_single_particle_selection.method 'INTERACTIVE' _em_single_particle_selection.details . _em_single_particle_selection.citation_id 1 ; save_ save__em_single_particle_selection.selection_id _item_description.description ; The value of _em_single_particle_selection.selection_id identifies the general set of selection conditions associated with specific single particle selection conditions described in this category. The value of _em_single_particle_selection.selection_id points to the _em_particle_selection.id in the EM_PARTICLE_SELECTION category. ; _item.name '_em_single_particle_selection.selection_id' _item.category_id em_single_particle_selection _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_single_particle_selection.selection_id' _item_linked.parent_name '_em_particle_selection.id' save_ save__em_single_particle_selection.num_micrographs _item_description.description ; The number of micrographs used ; _item.name '_em_single_particle_selection.num_micrographs' _item.category_id em_single_particle_selection _item.mandatory_code no _item_type.code int save_ save__em_single_particle_selection.num_particles _item_description.description ; The number of particles selected from the projection set of images. ; _item.name '_em_single_particle_selection.num_particles' _item.category_id em_single_particle_selection _item.mandatory_code no _item_type.code int _item_examples.case 840 save_ save__em_single_particle_selection.protocol _item_description.description ; The protocol used for selecting observed assemblies. ; _item.name '_em_single_particle_selection.protocol' _item.category_id em_single_particle_selection _item.mandatory_code no _item_type.code text save_ save__em_single_particle_selection.method _item_description.description ; The method used for selecting observed assemblies. ; _item.name '_em_single_particle_selection.method' _item.category_id em_single_particle_selection _item.mandatory_code no _item_type.code text _item_examples.case 'particles picked interactively from monitor' save_ save__em_single_particle_selection.details _item_description.description ; Any additional details used for selecting observed assemblies. ; _item.name '_em_single_particle_selection.details' _item.category_id em_single_particle_selection _item.mandatory_code no _item_type.code text _item_examples.case 'negative monitor contrast facilitated particle picking' save_ save__em_single_particle_selection.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_single_particle_selection.citation_id' _item.category_id em_single_particle_selection _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_single_particle_selection.citation_id' _item_linked.parent_name '_citation.id' save_ ######################### # EM_HELICAL_SELECTION # ######################### save_em_helical_selection _category.description ; Data items in the EM_HELICAL_SELECTION category record details for the selection of helical or filament particle types. ; _category.id em_helical_selection _category.mandatory_code yes _category_key.name '_em_helical_selection.selection_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_image_selection_group' 'em_helical_group' save_ save__em_helical_selection.selection_id _item_description.description ; The value of _em_helical_selection.selection_id identifies the general set of selection conditions associated with specific filament selection conditions described in this category. The value of _em_filament_particle_selection.selection_id points to the _em_particle_selection.id in the EM_PARTICLE_SELECTION category. ; _item.name '_em_helical_selection.selection_id' _item.category_id em_helical_selection _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_helical_selection.selection_id' _item_linked.parent_name '_em_particle_selection.id' save_ save__em_helical_selection.num_unit_cells _item_description.description ; The numeber of unit cells or asymmetric units used to refine the repeat parameters ; _item.name '_em_helical_selection.num_unit_cells' _item.category_id em_helical_selection _item.mandatory_code no _item_type.code int save_ save__em_helical_selection.num_helices _item_description.description ; The numeber of number of helices used used to refine the repeat parameters ; _item.name '_em_helical_selection.num_helices' _item.category_id em_helical_selection _item.mandatory_code no _item_type.code int save_ #save__em_helical_selection.straightening_details # _item_description.description #; Details on the method used to determine the path of the helical # axis and thus correct curvature in the filaments. #; # _item.name '_em_helical_selection.straightening_details' # _item.category_id em_helical_selection # _item.mandatory_code no # _item_type.code text # _item_examples.case #; The filament axis was identified by first orienting the template # to match the local orientation of a short segment of the original # filament and then calculating a cross correlation between the # reoriented template and this short segment of filament. This # procedure is then repeated along the length of the filament. # We have implemented such a procedure by having the user trace # the approximate filament axis through identification a few points # along the filament. A spline curve fitted to this axis provides # the approximate local curvature of each filament segment. #; # save_ #save__em_helical_selection.box_criteria # _item_description.description #; The box criteria for tubes used in the 3d reconstruction for # the helical assembly. # For three-dimensional structure determination tubes are treated # as helical objects and analysed by dividing them into axail repeat # lengths, echa of which contains a complete set of views,e.g. The # tube is first divided into (overlapping) portions, each corresponding # to one axial repeat in length. Areas of tube boxed off from the digitised # images and interpolated in real space so that after refinement an exact # multiple of the axial repeat distance would be included in the Fourier # transform. This means all the layer-lines fall exactly on the transform # grid, while maintaining a constant sampling along the layer-lines so that # different images can be easily compared. # The whole repeats are boxed off and aligned against # the reference dataset using Fourier terms extending only to the # first or second zero in the CTF. Next the whole repeats are # divided up into half-segments (length approximately equal to the # radius of the tube), and the half segments are aligned against # the reference data set. Finally the the segments themselves, in # orientations determined from the half-segment alignment are # refined against the reference dataset. Seven parameters are # obtained for each segment: orientation in the image plane; # out-of-plane tilt;effective repeat length; width relative to that # of the reference;transverse, longitudinal and azimuthal # alignments of the origin. #; # _item.name '_em_helical_selection.box_criteria' # _item.category_id em_helical_selection # _item.mandatory_code no # _item_type.code line # save_ ############################ # EM_2D_CRYSTAL_SELECTION # ############################ save_em_2d_crystal_selection _category.description ; Data items in the EM_2D_CRYSTAL_SELECTION category record details for the selection of 2D crystals. ; _category.id em_2d_crystal_selection _category.mandatory_code yes _category_key.name '_em_2d_crystal_selection.selection_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_image_selection_group' 'em_2D_crystal_group' save_ save__em_2d_crystal_selection.selection_id _item_description.description ; The value of _em_2d_crystal_selection.selection_id identifies the general set of selection conditions associated with specific filament selection conditions described in this category. The value of _em_2d_crystal_selection.selection_id points to the _em_particle_selection.id in the EM_PARTICLE_SELECTION category. ; _item.name '_em_2d_crystal_selection.selection_id' _item.category_id em_2d_crystal_selection _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_2d_crystal_selection.selection_id' _item_linked.parent_name '_em_particle_selection.id' save_ save__em_2d_crystal_selection.details _item_description.description ; Any additional details used for selecting 2d crystals. ; _item.name '_em_2d_crystal_selection.details' _item.category_id em_2d_crystal_selection _item.mandatory_code no _item_type.code text _item_examples.case 'negative monitor contrast facilitated particle picking' save_ ########################## ## EM_3D_RECONSTRUCTION ## ########################## save_em_3d_reconstruction _category.description ; Data items in the EM_3D_RECONSTRUCTION category record details of the 3D reconstruction procedure from 2D projections. ; _category.id em_3d_reconstruction _category.mandatory_code no loop_ _category_key.name '_em_3d_reconstruction.entry_id' '_em_3d_reconstruction.id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_reconstruction_group' 'em_single_particle_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_3d_reconstruction.entry_id 1DYL _em_3d_reconstruction.id 1 _em_3d_reconstruction.method 'CROSS-COMMON LINES' _em_3d_reconstruction.citation_id 1 _em_3d_reconstruction.details . _em_3d_reconstruction.resolution 9 _em_3d_reconstruction.resolution_method . _em_3d_reconstruction.ctf_correction_method . _em_3d_reconstruction.nominal_pixel_size 2.64 _em_3d_reconstruction.actual_pixel_size 2.52 ; save_ save__em_3d_reconstruction.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_3d_reconstruction.entry_id' _item.category_id em_3d_reconstruction _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_3d_reconstruction.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_3d_reconstruction.id _item_description.description ; The value of _em_3d_reconstruction.id must uniquely identify the 3d reconstruction. ; _item.name '_em_3d_reconstruction.id' _item.category_id em_3d_reconstruction _item.mandatory_code yes _item_type.code code save_ save__em_3d_reconstruction.num_particles _item_description.description ; The number of particles used in the 3d reconstruction ; _item.name '_em_3d_reconstruction.num_particles' _item.category_id em_3d_reconstruction _item.mandatory_code yes _item_type.code int save_ save__em_3d_reconstruction.details _item_description.description ; General details on the 3d recontruction ; _item.name '_em_3d_reconstruction.details' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text loop_ _item_examples.case _item_examples.detail 1 ; Orientation determination using the random-conical data collection method. This method uses a defined geometry in the data collection, and is able to find the handedness of the structure unambiguously. Each specimen field is imaged twice, once tilted, once untilted. Particles are selected simultaneously from both untilted- and tilted-specimen fields, using a special interactive particle-selection program that is able to "predict" the location of a particle in the tilted-specimen field when its counterpart has been selected in the untilted field. From the untilted-specimen particle data set, all particles are selected that exhibit the same view. This can be done by using alignment followed by classification. The corresponding tilted-specimen data subset can be used to compute a reconstruction: the orientations of the tilted-particle projections lie on a cone with fixed angle (the tilt angle) and random azimuths (the in-plane angles found in the alignment of the untilted particle set). ; 2 ; Orientation determination using common lines (a.k.a. "angular reconstitution"). This method is based on the fact that in Fourier space any two projections intersect along a central line ("the common line"). Hence, in principle, the relative orientations between three projections can be determined - except that the handedness of the constellation is ambiguous. Because of the low signal-to-noise ratio of raw particle images, averages of projections falling into roughly the same orientation must be used. Since the procedure leads to solutions presenting local minima, it must be repeated several times to find solutions that form a cluster, presumably around the global minimum. Such clustering of solutions can be detected by multivariate statistical analysis of the resulting 3D maps. Two clusters are expected, one for each enantiomorph. After initial structure is obtained, it should be further refined using 3D projection matching strategy described next. ; 3 ; Orientation determination by 3D projection matching. Here the existing 3D map is projected in many orientations on a regular angular grid, and the resulting projections that are compared, one by one, with each of the experimental projections. This comparison (by cross-correlation ) yields a refined set of Eulerian angles , with which a refined reconstruction can be computed using one of the possible reconstruction techniques. This procedure requires iteration until the angles for each projection stabilize. ; save_ save__em_3d_reconstruction.method_details _item_description.description ; The algorithm method used for the 3d-reconstruction. e.g. Random-conical reconstruction: a method of data collection and reconstruction used for single particles, typically used initially in a project, to obtain a first low-resolution reconstruction of the macromolecule [Radermacher et al., 1987]. Two images of the same specimen field are collected, one with untilted grid, the other with the grid tilted by 50 to 60 degrees. Any set of particles presenting the same view in the untilted-specimen image form a random-conical projection set in the associated tilted-specimen image. Helical reconstruction Helical reconstruction is used when the protein of interest forms a natural helix. Since the helix is a recurring structure with a very well defined pattern, the repeating pattern of the helix can be exploited to solve the structure. In this case, no alignment of the particles is needed, since the individual positions of subunits within the helix are clearly defined by the shape of the helix. Two common examples of structures solved by helical reconstruction are TMV and microtubules. Icosahedral reconstruction Icosahedral reconstructions also take advantage of internal symmetry and repetition to generate a detailed three-dimensional structure from the data set. In this case, the symmetry is icosahedral (twenty-one sided). Many viruses exhibit icosahedral symmetry in their capsid proteins, and this method has been used to solve their structures. Electron crystallography Electron crystallography is similar to x-ray crystallography in that it exploits the repeating pattern found within a crystal to generate a structure. Just as with x-ray crystallography, difraction patterns are generated and are used to define an electron density map. However, it differs in that the crystal used is a two-dimensional sheet as opposed to three three-dimensional crystals of x-ray crystallography. Common Lines Another reconstruction method searches for the intersection of any two projections in Fourier space. The Fourier transform of the experimental projections all form slices around a common core in Fourier space. Therefore, the intersection of these projections are unique (unless the projections perfectly overlap), and their relative orientation can be found when three or more projections are used. A principal problem with this method is that the handedness of the image is lost. This, however, can later be corrected by visual examination of the model with other known structural information. Back Projection As its name implies, back projection is the inverse function of projection. When an n-dimensional object is projected, each projection is an n-1 dimensional sum of its density along the projection axis. Therefore, a sphere would have circles as its projections. A cube, on the other hand, would produce either squares, diamonds, or other intermediate parallelograms depending on the direction of projection. The actual shape, of course, depends on the orientation from which the projection was made. The reverse function is called back projection and regenerates the original object. ; _item.name '_em_3d_reconstruction.method_details' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text _item_examples.case 'cross-common lines' save_ save__em_3d_reconstruction.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_3d_reconstruction.citation_id' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_3d_reconstruction.citation_id' _item_linked.parent_name '_citation.id' save_ save__em_3d_reconstruction.resolution _item_description.description ; The final resolution (in angstroms)of the 3d reconstruction. ; _item.name '_em_3d_reconstruction.resolution' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__em_3d_reconstruction.resolution_method_details _item_description.description ; The method used to determine the final resolution of the 3d reconstruction. The Fourier Shell Correlation criterion as a measure of resolution is based on the concept of splitting the (2D) data set into two halves; averaging each and comparing them using the Fourier Ring Correlation (FRC) technique. ; _item.name '_em_3d_reconstruction.resolution_method_details' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text _item_examples.case 'FSC at 0.5 cut-off' save_ save__em_3d_reconstruction.amplitude_correction_details _item_description.description ; The Amplitude correction method. Frequency amplitude correction with X-ray scattering data enhances the Fourier amplitudes of a reconstructed cryo-EM volume so they more closely resemble those of experimental low-angle X-ray scattering data. Normal amplitude correction (in which case the SNR weighted averaging of particles will still occur properly) may be applied or without it, in which case the (phase-flipped) data is not corrected during averaging, then the final 3D model is 'fixed'. ; _item.name '_em_3d_reconstruction.amplitude_correction_details' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text save_ save__em_3d_reconstruction.b-factor_correction_details _item_description.description ; Details of the B-factor correction method. ; _item.name '_em_3d_reconstruction.b-factor_correction_details' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text save_ save__em_3d_reconstruction.envelope_function_correction_details _item_description.description ; Details of the envelope function correction method. ; _item.name '_em_3d_reconstruction.envelope_function_correction_details' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text save_ save__em_3d_reconstruction.ctf_correction_method_details _item_description.description ; The CTF-correction method. The Contrast Transfer Function CTF compensation for low contrast specimens (e.g. frozen-hydrated), for which phase contrast is the only significant mechanism, then higher defocus levels must be used to achieve any significant transfer, and several images at different focus levels must be combined to complete the information lost from the transfer gaps of any one image. The CTF correction can be applied to each extracted particle separately or to the whole micrograph after digitisation. The simplest level of compensation is to reverse phases at the negative lobes of the CTF. ; _item.name '_em_3d_reconstruction.ctf_correction_method_details' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text _item_examples.case 'CTF correction of each particle' save_ save__em_3d_reconstruction.local_symmetry_detail _item_description.description ; General details describing any local or approximate symmetry used in the single particle reconstruction ; _item.name '_em_3d_reconstruction.local_symmetry_detail' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text save_ save__em_3d_reconstruction.num_asymmetric_units _item_description.description ; The number of asymmetric units used in the single particle reconstruction ; _item.name '_em_3d_reconstruction.num_asymmetric_units' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code int save_ save__em_3d_reconstruction.voxel_size_x _item_description.description ; The actual pixel size of projection set of images in x IF only _em_3d_reconstruction.voxel_size_x is given then a cube is assumed. ; _item.name '_em_3d_reconstruction.voxel_size_x' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code float save_ save__em_3d_reconstruction.voxel_size_y _item_description.description ; The actual pixel size of projection set of images in y IF only _em_3d_reconstruction.voxel_size_x is given then a cube is assumed. ; _item.name '_em_3d_reconstruction.voxel_size_y' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code float save_ save__em_3d_reconstruction.voxel_size_z _item_description.description ; The actual pixel size of projection set of images in z IF only _em_3d_reconstruction.voxel_size_x is given then a cube is assumed. ; _item.name '_em_3d_reconstruction.voxel_size_z' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code float save_ save__em_3d_reconstruction.helix_straightening_details _item_description.description ; Details on how located layer lines are used to choose a selection rule which best fits the data. Based on this selection rule the filament is then reboxed and restraightened using the original digitized image so that the final image contains an integral number of helical repeats. The selection rule define helical lattices which relate the layer- line number l to the order of the Bessel function, n, contributing to the layer-line. (n is the start number, ie number around the circumference, of the contributing helix). The diffraction pattern from a helix consists not of discrete spots but of difraction spots which have been broadened into layer-lines. The order of the Bessel functions allowed to contribute to the diffraction pattern of a helix on a given layer line versus the layer line along the ordinate gives a function which is described by a lattice. Such a plot is analogous to the diffraction pattern from a planar array corresponding to a flattened helix and is called an (n,l) plot. e.g. the n,l plot corresponding to the selection rule l = 5n + 12m where m is an integer and indicates e.g. 12 (ribosomes) per repeat five turns long, whilst the n,l plot corresponding to the selection rule l = 5n + 17m indicates 17(ribosomes) per repeat five turns along. ; _item.name '_em_3d_reconstruction.helix_straightening_details' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text save_ save__em_3d_reconstruction.helix_number_datasets _item_description.description ; The number of datasets used in the 3d reconstruction for the helical assembly. ; _item.name '_em_3d_reconstruction.helix_number_datasets' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code int save_ save__em_3d_reconstruction.helix_average_phase_residual _item_description.description ; The average phase residual for the helical assembly. ; _item.name '_em_3d_reconstruction.helix_average_phase_residual' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code float save_ save__em_3d_reconstruction.helix_layerline_d_res_high _item_description.description ; The layer-line resolution. Layer-lines fade out and are only visible to a certain resolution. ; _item.name '_em_3d_reconstruction.helix_layerline_d_res_high' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code line save_ ################### ## EM_3D_FITTING ## ################### save_em_3d_fitting _category.description ; Data items in the 3D_FITTING category record details of the method of fitting atomic coordinates from a PDB file into a 3d-em volume map file ; _category.id em_3d_fitting _category.mandatory_code no loop_ _category_key.name '_em_3d_fitting.id' '_em_3d_fitting.entry_id' loop_ _category_group.id 'em_group' 'inclusive_group' 'em_structure_analysis_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - EMDB entry EM1078 ; ; loop_ _em_3d_fitting.id _em_3d_fitting.entry_id _em_3d_fitting.method _em_3d_fitting.target_criteria _em_3d_fitting.over_all_b_value _em_3d_fitting.ref_space _em_3d_fitting.ref_protocol _em_3d_fitting.details 1 EM1078 AUTOMATIC . . REAL 'RIGID BODY REFINEMENT' . 2 EM1078 AUTOMATIC . . REAL 'RIGID BODY REFINEMENT' . 3 EM1078 AUTOMATIC . . REAL 'RIGID BODY REFINEMENT' . ; ; Example 2 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_3d_fitting.id 1 _em_3d_fitting.entry_id 1DYL _em_3d_fitting.method AUTOMATIC _em_3d_fitting.target_criteria R-FACTOR _em_3d_fitting.over_all_b_value . _em_3d_fitting.ref_space REAL _em_3d_fitting.ref_protocol 'RIGID BODY REFINEMENT' _em_3d_fitting.details ; THE CRYSTAL STRUCTURE OF THE CAPSID PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27:345-359 (SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE FOUR INDEPENDENT MONOMER DENSITIES BETWEEN THE INNER LEAFLET OF THE BILAYER AND THE RNA. THESE POSITIONS WERE THEN REFINED BY RIGID BODY REFINEMENT IN REAL SPACE WITH THE PROGRAM EMFIT (CHENG ET AL. 1995, CELL 80, 621-630). THE QUALITY OF THE FIT CAN BE SEEN FROM THE MAP DENSITY WITHIN THE PROTEIN. ALL 4563 ATOMS ARE IN DENSITY OF AT LEAST 4 SIGMA (96.73) ABOVE THE AVERAGE (512.04), 1167 ATOMS ARE IN DENSITY BETWEEN 4 AND 5 SIGMA, 3174 ATOMS ARE IN DENSITY BETWEEN 5 AND 6 SIGMA, AND 222 ATOMS ARE IN DENSTY OF 6 SIGMA OR ABOVE. THE VARIATION IN DENSITY OVER THE FITTED PROTEIN CAN BE VISUALIZED WITH THE PSEUDO TEMPERATURE FACTOR. THE DENSITY VALUE AT EACH ATOM IS GIVEN IN THE 8TH COLUM (USUALLY THE OCCUPANCY) AS THE NUMBER OF STANDARD DEVIATION ABOVE BACKGROUND. COLUMN NINE (USUALLY THE TEMPERATURE FACTOR) CONTAINS THE VALUE OF THE RELATIVE DENSITY WITHIN THE FITTED PROTEIN SCALED LINEARLY SO THAT THE MINIMUM DENSITY IS 100.0 AND THE MAXIMUM DENSITY IS 1.0. THE ATOMS THAT LIE IN THE LOWER DENSITY REGIONS WILL HAVE THE HIGHEST PSEUDO TEMPERATURE FACTORS. ; ; save_ save__em_3d_fitting.id _item_description.description ; The value of _em_3d_fitting.id must uniquely identify a fitting procedure of atomic coordinates into 3dem reconstructed volume map. ; loop_ _item.name _item.category_id _item.mandatory_code '_em_3d_fitting.id' em_3d_fitting yes '_em_3d_fitting_list.3d_fitting_id' em_3d_fitting_list yes loop_ _item_linked.child_name _item_linked.parent_name '_em_3d_fitting_list.3d_fitting_id' '_em_3d_fitting.id' _item_type.code code save_ save__em_3d_fitting.entry_id _item_description.description ; This data item is a pointer to _entry_id in the ENTRY category. ; _item.name '_em_3d_fitting.entry_id' _item.category_id em_3d_fitting _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_3d_fitting.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_3d_fitting.method _item_description.description ; The method used to fit atomic coordinates into the 3dem reconstructed map. ; _item.name '_em_3d_fitting.method' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code line save_ save__em_3d_fitting.target_criteria _item_description.description ; The quality of fit of the atomic coordinates into the 3dem volume map. ; _item.name '_em_3d_fitting.target_criteria' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code text _item_examples.case 'best visual fit using the program O' save_ #save__em_3d_fitting.quality_index # _item_description.description #; The quality of fit of the atomic coordinates into the # 3dem volume map. #; # _item.name '_em_3d_fitting.quality_index' # _item.category_id em_3d_fitting # _item.mandatory_code no # _item_type.code text # save_ # save__em_3d_fitting.local_variance _item_description.description ; Description of local variance of fit of the atomic coordinates into the 3dem volume map. ; _item.name '_em_3d_fitting.local_variance' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code text save_ save__em_3d_fitting.quality_details _item_description.description ; Description of the quality of fit of the atomic coordinates into the 3dem volume map. ; _item.name '_em_3d_fitting.quality_details' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code text save_ save__em_3d_fitting.details _item_description.description ; Any additional details regarding fitting of atomic coordinates into the 3d-em volume. ; _item.name '_em_3d_fitting.details' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code text _item_examples.case 'partial' save_ save__em_3d_fitting.overall_b_value _item_description.description ; The overall B (temperature factor) value for the 3d-em volume. ; _item.name '_em_3d_fitting.overall_b_value' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code float save_ save__em_3d_fitting.ref_space _item_description.description ; A flag to indicate whether fitting was carried out in real or reciprocal refinement space. ; _item.name '_em_3d_fitting.ref_space' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value REAL RECIPROCAL save_ save__em_3d_fitting.ref_protocol _item_description.description ; The type of protocol used in the refinement. ; _item.name '_em_3d_fitting.ref_protocol' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code text _item_examples.case 'rigid body' save_ ######################## ## EM_3D_FITTING_LIST ## ######################## save_em_3d_fitting_list _category.description ; Data items in the 3D_FITTING_LIST category lists the methods of fitting atomic coordinates from a PDB file into a 3d-em volume map file ; _category.id em_3d_fitting_list _category.mandatory_code no loop_ _category_key.name '_em_3d_fitting_list.id' '_em_3d_fitting_list.3d_fitting_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_structure_analysis_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on EM entry 1078 ; ; loop_ _em_3d_fitting_list.id _em_3d_fitting_list.3d_fitting_id _em_3d_fitting_list.entry_id _em_3d_fitting_list.pdb_entry_id _em_3d_fitting_list.pdb_chain_id _em_3d_fitting_list.start_seq _em_3d_fitting_list.end_seq _em_3d_fitting_list.fitted_pdb_entry_id _em_3d_fitting_list.fitted_pdb_chain_id _em_3d_fitting_list.start_pdb_symm_as_xyz _em_3d_fitting_list.transform_matrix[1][1] _em_3d_fitting_list.transform_matrix[1][2] _em_3d_fitting_list.transform_matrix[1][3] _em_3d_fitting_list.transform_matrix[1][4] _em_3d_fitting_list.transform_matrix[2][1] _em_3d_fitting_list.transform_matrix[2][2] _em_3d_fitting_list.transform_matrix[2][3] _em_3d_fitting_list.transform_matrix[2][4] _em_3d_fitting_list.transform_matrix[3][1] _em_3d_fitting_list.transform_matrix[3][2] _em_3d_fitting_list.transform_matrix[3][3] _em_3d_fitting_list.transform_matrix[3][4] _em_3d_fitting_list.transform_matrix[4][1] _em_3d_fitting_list.transform_matrix[4][2] _em_3d_fitting_list.transform_matrix[4][3] _em_3d_fitting_list.transform_matrix[4][4] 1 1 EM1078 1EL6 A 1 219 1PDF A 'x, y, z' . . . . . . . . . . . . 2 1 EM1078 1EL6 B 1 219 1PDF B 'x, y, z' . . . . . . . . . . . . 3 1 EM1078 1EL6 C 1 219 1PDF C 'x, y, z' . . . . . . . . . . . . 4 1 EM1078 1EL6 A 1 219 1PDF D 'x, y, z' . . . . . . . . . . . . 5 1 EM1078 1EL6 B 1 219 1PDF E 'x, y, z' . . . . . . . . . . . . 6 1 EM1078 1EL6 C 1 219 1PDF F 'x, y, z' . . . . . . . . . . . . 7 1 EM1078 1EL6 A 1 219 1PDF G 'x, y, z' . . . . . . . . . . . . 8 1 EM1078 1EL6 B 1 219 1PDF H 'x, y, z' . . . . . . . . . . . . 9 1 EM1078 1EL6 C 1 219 1PDF I 'x, y, z' . . . . . . . . . . . . 10 1 EM1078 1EL6 A 1 219 1PDF J 'x, y, z' . . . . . . . . . . . . 11 1 EM1078 1EL6 B 1 219 1PDF K 'x, y, z' . . . . . . . . . . . . 12 1 EM1078 1EL6 C 1 219 1PDF L 'x, y, z' . . . . . . . . . . . . 13 1 EM1078 1EL6 A 1 219 1PDF M 'x, y, z' . . . . . . . . . . . . 14 1 EM1078 1EL6 B 1 219 1PDF N 'x, y, z' . . . . . . . . . . . . 15 1 EM1078 1EL6 C 1 219 1PDF O 'x, y, z' . . . . . . . . . . . . 16 1 EM1078 1EL6 A 1 219 1PDF P 'x, y, z' . . . . . . . . . . . . 17 1 EM1078 1EL6 B 1 219 1PDF Q 'x, y, z' . . . . . . . . . . . . 18 1 EM1078 1EL6 C 1 219 1PDF R 'x, y, z' . . . . . . . . . . . . 19 2 EM1078 1H6W A 250 397 1PDI A 'x, y, z' . . . . . . . . . . . . 20 2 EM1078 1OCY A 397 527 1PDI A 'x, y, z' . . . . . . . . . . . . 21 2 EM1078 1H6W A 250 397 1PDI B '1-y, 1+x-y, z' . . . . . . . . . . . . 22 2 EM1078 1OCY A 397 527 1PDI B '1-y, 1+x-y, z' . . . . . . . . . . . . 23 2 EM1078 1H6W A 250 397 1PDI C 'y-x, 1-x, z' . . . . . . . . . . . . . 24 2 EM1078 1OCY A 397 527 1PDI C 'y-x, 1-x, z' . . . . . . . . . . . . . 25 2 EM1078 1H6W A 250 397 1PDI D 'x, y, z' . . . . . . . . . . . . 26 2 EM1078 1OCY A 397 527 1PDI D 'x, y, z' . . . . . . . . . . . . 27 2 EM1078 1H6W A 250 397 1PDI E '1-y, 1+x-y, z' . . . . . . . . . . . . 28 2 EM1078 1OCY A 397 527 1PDI E '1-y, 1+x-y, z' . . . . . . . . . . . . 29 2 EM1078 1H6W A 250 397 1PDI F 'y-x, 1-x, z' . . . . . . . . . . . . 30 2 EM1078 1OCY A 397 527 1PDI F 'y-x, 1-x, z' . . . . . . . . . . . . 31 2 EM1078 1H6W A 250 397 1PDI G 'x, y, z' . . . . . . . . . . . . 32 2 EM1078 1OCY A 397 527 1PDI G 'x, y, z' . . . . . . . . . . . . 33 2 EM1078 1H6W A 250 397 1PDI H '1-y, 1+x-y, z' . . . . . . . . . . . . 34 2 EM1078 1OCY A 397 527 1PDI H '1-y, 1+x-y, z' . . . . . . . . . . . . 35 2 EM1078 1H6W A 250 397 1PDI I 'y-x, 1-x, z' . . . . . . . . . . . . 36 2 EM1078 1OCY A 397 527 1PDI I 'y-x, 1-x, z' . . . . . . . . . . . . 37 2 EM1078 1H6W A 250 397 1PDI J 'x, y, z' . . . . . . . . . . . . 38 2 EM1078 1OCY A 397 527 1PDI J 'x, y, z' . . . . . . . . . . . . 39 2 EM1078 1H6W A 250 397 1PDI K '1-y, 1+x-y, z' . . . . . . . . . . . . 40 2 EM1078 1OCY A 397 527 1PDI K '1-y, 1+x-y, z' . . . . . . . . . . . . 41 2 EM1078 1H6W A 250 397 1PDI L 'y-x, 1-x, z' . . . . . . . . . . . . 42 2 EM1078 1OCY A 397 527 1PDI L 'y-x, 1-x, z' . . . . . . . . . . . . 43 2 EM1078 1H6W A 250 397 1PDI M 'x, y, z' . . . . . . . . . . . . 44 2 EM1078 1OCY A 397 527 1PDI M 'x, y, z' . . . . . . . . . . . . 45 2 EM1078 1H6W A 250 397 1PDI N '1-y, 1+x-y, z' . . . . . . . . . . . . 46 2 EM1078 1OCY A 397 527 1PDI N '1-y, 1+x-y, z' . . . . . . . . . . . . 47 2 EM1078 1H6W A 250 397 1PDI O 'y-x, 1-x, z' . . . . . . . . . . . . 48 2 EM1078 1OCY A 397 527 1PDI O 'y-x, 1-x, z' . . . . . . . . . . . . 49 2 EM1078 1H6W A 250 397 1PDI P 'x, y, z' . . . . . . . . . . . . 50 2 EM1078 1OCY A 397 527 1PDI P 'x, y, z' . . . . . . . . . . . . 51 2 EM1078 1H6W A 250 397 1PDI Q '1-y, 1+x-y, z' . . . . . . . . . . . . 52 2 EM1078 1OCY A 397 527 1PDI Q '1-y, 1+x-y, z' . . . . . . . . . . . . 53 2 EM1078 1H6W A 250 397 1PDI R 'y-x, 1-x, z' . . . . . . . . . . . . 54 2 EM1078 1OCY A 397 527 1PDI R 'y-x, 1-x, z' . . . . . . . . . . . . 55 3 EM1078 1QEX A 1 288 1PDP A 'x, y, z' . . . . . . . . . . . . 56 3 EM1078 1QEX B 1 288 1PDP B 'x, y, z' . . . . . . . . . . . . 57 3 EM1078 1QEX A 1 288 1PDP C '-y, x-y, z' . . . . . . . . . . . . 58 3 EM1078 1QEX B 1 288 1PDP D '-y, x-y, z' . . . . . . . . . . . . 59 3 EM1078 1QEX A 1 288 1PDP E 'y-x, -x, z' . . . . . . . . . . . . 60 3 EM1078 1QEX B 1 288 1PDP F 'y-x, -x, z' . . . . . . . . . . . . 61 3 EM1078 1QEX A 1 288 1PDP G 'x, y, z' . . . . . . . . . . . . 62 3 EM1078 1QEX B 1 288 1PDP H 'x, y, z' . . . . . . . . . . . . 63 3 EM1078 1QEX A 1 288 1PDP I '-y, x-y, z' . . . . . . . . . . . . 64 3 EM1078 1QEX B 1 288 1PDP J '-y, x-y, z' . . . . . . . . . . . . 65 3 EM1078 1QEX A 1 288 1PDP K 'y-x, -x, z' . . . . . . . . . . . . 66 3 EM1078 1QEX B 1 288 1PDP L 'y-x, -x, z' . . . . . . . . . . . . 67 3 EM1078 1QEX A 1 288 1PDP M 'x, y, z' . . . . . . . . . . . . 68 3 EM1078 1QEX B 1 288 1PDP N 'x, y, z' . . . . . . . . . . . . 69 3 EM1078 1QEX A 1 288 1PDP O '-y, x-y, z' . . . . . . . . . . . . 70 3 EM1078 1QEX B 1 288 1PDP P '-y, x-y, z' . . . . . . . . . . . . 71 3 EM1078 1QEX A 1 288 1PDP Q 'y-x, -x, z' . . . . . . . . . . . . 72 3 EM1078 1QEX B 1 288 1PDP R 'y-x, -x, z' . . . . . . . . . . . . ; save_ save__em_3d_fitting_list.id _item_description.description ; This data item is a unique identifier. ; _item.name '_em_3d_fitting_list.id' _item.category_id em_3d_fitting_list _item.mandatory_code yes _item_type.code code save_ save__em_3d_fitting_list.3d_fitting_id _item_description.description ; The value of _em_3d_fitting_list.3d_fitting_id is a pointer to _em_3d_fitting.id in the 3d_fitting category ; _item.name '_em_3d_fitting_list.3d_fitting_id' _item.mandatory_code yes save_ save__em_3d_fitting_list.pdb_entry_id _item_description.description ; The PDB code for the entry used in fitting. ; _item.name '_em_3d_fitting_list.pdb_entry_id' _item.category_id em_3d_fitting_list _item.mandatory_code no _item_type.code line _item_linked.child_name '_em_3d_fitting_list.pdb_entry_id' _item_linked.parent_name '_entry.id' save_ save__em_3d_fitting_list.pdb_chain_id _item_description.description ; The chain id for the entry used in fitting. ; _item.name '_em_3d_fitting_list.pdb_chain_id' _item.category_id em_3d_fitting_list _item.mandatory_code no _item_type.code code save_ save__em_3d_fitting_list.model_details _item_description.description ; Description of a particular component pdb entry used in fitting. ; _item.name '_em_3d_fitting_list.model_details' _item.category_id em_3d_fitting_list _item.mandatory_code no _item_type.code text save_ save__em_3d_fitting_list.fitted_pdb_entry_id _item_description.description ; The PDB code for the entry produced by the fitting. ; _item.name '_em_3d_fitting_list.fitted_pdb_entry_id' _item.category_id em_3d_fitting_list _item.mandatory_code no _item_type.code line _item_linked.child_name '_em_3d_fitting_list.fitted_pdb_entry_id' _item_linked.parent_name '_entry.id' save_ save__em_3d_fitting_list.entry_id _item_description.description ; The EM entry id pointer ; _item.name '_em_3d_fitting_list.entry_id' _item.category_id em_3d_fitting_list _item.mandatory_code no _item_type.code line _item_linked.child_name '_em_3d_fitting_list.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_3d_fitting_list.fitted_pdb_chain_id _item_description.description ; The chain id for the resulting fitted coordinates ; _item.name '_em_3d_fitting_list.fitted_pdb_chain_id' _item.category_id em_3d_fitting_list _item.mandatory_code no _item_type.code code save_ save__em_3d_fitting_list.start_seq _item_description.description ; The start sequence ID for the pdb entry chain used in the fitting ; _item.name '_em_3d_fitting_list.start_seq' _item.category_id em_3d_fitting_list _item.mandatory_code no _item_type.code code save_ save__em_3d_fitting_list.end_seq _item_description.description ; The end sequence ID for the pdb entry chain used in the fitting ; _item.name '_em_3d_fitting_list.end_seq' _item.category_id em_3d_fitting_list _item.mandatory_code no _item_type.code code save_ save__em_3d_fitting_list.start_pdb_symm_as_xyz _item_description.description ; The symmetry required to be applied to the starting PDB entry chain before starting the fitting procedure ; _item.name '_em_3d_fitting_list.start_pdb_symm_as_xyz' _item.category_id em_3d_fitting_list _item.mandatory_code no _item_type.code line save_ save__em_3d_fitting_list.transform_matrix[1][1] _item_description.description ; The (1,1) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement ; _item.name '_em_3d_fitting_list.transform_matrix[1][1]' _item.mandatory_code no _item.category_id em_3d_fitting_list _item_sub_category.id matrix _item_type.code float save_ save__em_3d_fitting_list.transform_matrix[1][2] _item_description.description ; The (1,2) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement ; _item.name '_em_3d_fitting_list.transform_matrix[1][2]' _item.mandatory_code no _item.category_id em_3d_fitting_list _item_sub_category.id matrix _item_type.code float save_ save__em_3d_fitting_list.transform_matrix[1][3] _item_description.description ; The (1,3) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement ; _item.name '_em_3d_fitting_list.transform_matrix[1][3]' _item.mandatory_code no _item.category_id em_3d_fitting_list _item_sub_category.id matrix _item_type.code float save_ save__em_3d_fitting_list.transform_matrix[1][4] _item_description.description ; The (1,4) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement ; _item.name '_em_3d_fitting_list.transform_matrix[1][4]' _item.mandatory_code no _item.category_id em_3d_fitting_list _item_sub_category.id matrix _item_type.code float save_ save__em_3d_fitting_list.transform_matrix[2][1] _item_description.description ; The (2,1) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement ; _item.name '_em_3d_fitting_list.transform_matrix[2][1]' _item.mandatory_code no _item.category_id em_3d_fitting_list _item_sub_category.id matrix _item_type.code float save_ save__em_3d_fitting_list.transform_matrix[2][2] _item_description.description ; The (2,2) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement ; _item.name '_em_3d_fitting_list.transform_matrix[2][2]' _item.mandatory_code no _item.category_id em_3d_fitting_list _item_sub_category.id matrix _item_type.code float save_ save__em_3d_fitting_list.transform_matrix[2][3] _item_description.description ; The (2,3) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement ; _item.name '_em_3d_fitting_list.transform_matrix[2][3]' _item.mandatory_code no _item.category_id em_3d_fitting_list _item_sub_category.id matrix _item_type.code float save_ save__em_3d_fitting_list.transform_matrix[2][4] _item_description.description ; The (2,4) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement ; _item.name '_em_3d_fitting_list.transform_matrix[2][4]' _item.mandatory_code no _item.category_id em_3d_fitting_list _item_sub_category.id matrix _item_type.code float save_ save__em_3d_fitting_list.transform_matrix[3][1] _item_description.description ; The (3,1) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement ; _item.name '_em_3d_fitting_list.transform_matrix[3][1]' _item.mandatory_code no _item.category_id em_3d_fitting_list _item_sub_category.id matrix _item_type.code float save_ save__em_3d_fitting_list.transform_matrix[3][2] _item_description.description ; The (3,2) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement ; _item.name '_em_3d_fitting_list.transform_matrix[3][2]' _item.mandatory_code no _item.category_id em_3d_fitting_list _item_sub_category.id matrix _item_type.code float save_ save__em_3d_fitting_list.transform_matrix[3][3] _item_description.description ; The (3,3) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement ; _item.name '_em_3d_fitting_list.transform_matrix[3][3]' _item.mandatory_code no _item.category_id em_3d_fitting_list _item_sub_category.id matrix _item_type.code float save_ save__em_3d_fitting_list.transform_matrix[3][4] _item_description.description ; The (3,4) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement ; _item.name '_em_3d_fitting_list.transform_matrix[3][4]' _item.mandatory_code no _item.category_id em_3d_fitting_list _item_sub_category.id matrix _item_type.code float save_ save__em_3d_fitting_list.transform_matrix[4][1] _item_description.description ; The (4,1) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement ; _item.name '_em_3d_fitting_list.transform_matrix[4][1]' _item.mandatory_code no _item.category_id em_3d_fitting_list _item_sub_category.id matrix _item_type.code float save_ save__em_3d_fitting_list.transform_matrix[4][2] _item_description.description ; The (4,2) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement ; _item.name '_em_3d_fitting_list.transform_matrix[4][2]' _item.mandatory_code no _item.category_id em_3d_fitting_list _item_sub_category.id matrix _item_type.code float save_ save__em_3d_fitting_list.transform_matrix[4][3] _item_description.description ; The (4,3) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement ; _item.name '_em_3d_fitting_list.transform_matrix[4][3]' _item.mandatory_code no _item.category_id em_3d_fitting_list _item_sub_category.id matrix _item_type.code float save_ save__em_3d_fitting_list.transform_matrix[4][4] _item_description.description ; The (4,4) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement ; _item.name '_em_3d_fitting_list.transform_matrix[4][4]' _item.mandatory_code no _item.category_id em_3d_fitting_list _item_sub_category.id matrix _item_type.code float save_ #################### ## EM_MICROGRAPHS ## #################### save_em_micrographs _category.description ; Data items in the EM_MICROGRAPHS category record details about em raw data images ; _category.id em_micrographs _category.mandatory_code no loop_ _category_key.name '_em_micrographs.image_id' '_em_micrographs.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_data_collection_group' save_ save__em_micrographs.image_id _item_description.description ; The value of _em_micrograph.image_id must uniquely identify an image used in the em experiments. ; _item.name '_em_micrographs.image_id' _item.category_id em_micrographs _item.mandatory_code yes _item_type.code code save_ save__em_micrographs.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_micrographs.entry_id' _item.category_id em_micrographs _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_micrographs.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_micrographs.microscope_id _item_description.description ; This data item is a pointer to _em_microscope.id in the EM_MICROSCOPE category. ; _item.name '_em_micrographs.microscope_id' _item.category_id em_micrographs _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_micrographs.microscope_id' _item_linked.parent_name '_em_microscope.id' save_ save__em_micrographs.specimen_id _item_description.description ; This data item is a pointer to _em_sample_preparation.id in the EM_SAMPLE_PREPARATION category. ; _item.name '_em_micrographs.specimen_id' _item.category_id em_micrographs _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_micrographs.specimen_id' _item_linked.parent_name '_em_sample_preparation.id' save_ save__em_micrographs.astigmatism_flag _item_description.description ; Astigmatism(axial): an electron-optical lens aberration that causes the defocus to be a function of azimuth, and the contrast transfer function to deviate from circular symmetry about the optical axis. As a consequence, the Thon rings deform into elliptic or hyperbolic patterns, depending on the size of defocus and the size of the astigmatic defocus difference. A flag for Y or N for astigmatism estimation ; _item.name '_em_micrographs.astigmatism_flag' _item.category_id em_micrographs _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value N NO Y YES save_ save__em_micrographs.circular_averaging_flag _item_description.description ; A flag for Y or N for circular averaging ; _item.name '_em_micrographs.circular_averaging_flag' _item.category_id em_micrographs _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value N NO Y YES save_ save__em_micrographs.image_filter _item_description.description ; The type of image filter used ; _item.name '_em_micrographs.image_filter' _item.category_id em_micrographs _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value Focus 'Far from focus' 'Near to focus' save_ save__em_micrographs.edge_threshold _item_description.description ; The threshold set for edge detection for carbon and ice images. ; _item.name '_em_micrographs.edge_threshold' _item.category_id em_micrographs _item.mandatory_code no _item_type.code text save_ save__em_micrographs.power_factor _item_description.description ; The upper cutoff frequency ; _item.name '_em_micrographs.power_factor' _item.category_id em_micrographs _item.mandatory_code no _item_type.code text save_ save__em_micrographs.averaging_overlap _item_description.description ; For each micrograph smaller images are cropped from the image with the power spectrum found for all small images and they are averaged to improve signal to noise ratio. ; _item.name '_em_micrographs.averaging_overlap' _item.category_id em_micrographs _item.mandatory_code no _item_type.code text save_ save__em_micrographs.field_size _item_description.description ; Field size refers to the width of each small image cropped. An _em_micrographs.averaging_overlap implies that the successive images have an overalp of (1-_em_micrographs.averaging_overlap)*field size. A higher value of _em_micrographs.averaging_overlap means a greater number of smaller images are used for averaging. If the signal to noise ratio is very low, the averaging overlap should be changed for better estimate of power spectrum. ; _item.name '_em_micrographs.field_size' _item.category_id em_micrographs _item.mandatory_code no _item_type.code text save_ save__em_micrographs.nominal_defocus _item_description.description ; The nominal defocus e.g. 2.00 ; _item.name '_em_micrographs.nominal_defocus' _item.category_id em_micrographs _item.mandatory_code no _item_type.code float save_ save__em_micrographs.refined_defocus_estimate _item_description.description ; The refined defocus estimate e.g. 1.975 ; _item.name '_em_micrographs.refined_defocus_estimate' _item.category_id em_micrographs _item.mandatory_code no _item_type.code float save_ save__em_micrographs.amplitude_contrast _item_description.description ; The amplitude contrast e.g. 0.06 ; _item.name '_em_micrographs.amplitude_contrast' _item.category_id em_micrographs _item.mandatory_code no _item_type.code float save_ save__em_micrographs.astigmatism_ratio _item_description.description ; The astigmatism ratio e.g. 0.96 ; _item.name '_em_micrographs.astigmatism_ratio' _item.category_id em_micrographs _item.mandatory_code no _item_type.code float save_ save__em_micrographs.correction_type _item_description.description ; The difference between the two is that in Phase only correction only the phase of the CTF is flipped whereas in Phase and Amplitude correction, Wiener filtering is done to correct both phase and amplitude. If the envelope function and noise spectrum parameters are not available then phase only correction is recommended. For example if the parameters calculated from far from focus images are used to correct near to focus images (after adjusting for the defocus difference), the envelope function and noise spectrum parameter estimates of far from focus images are not reliable for near to focus images. ; _item.name '_em_micrographs.correction_type' _item.category_id em_micrographs _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value 'Phase and Amplitude correction' 'Phase only correction' save_ save__em_micrographs.experiment_mode _item_description.description ; parameters of the CTF used for correcting are estimated from each image or parameters estimated for the far from images are used to correct near to focus images after compensating for the defocus ; _item.name '_em_micrographs.experiment_mode' _item.category_id em_micrographs _item.mandatory_code no _item_type.code text save_ save__em_micrographs.exposure_time _item_description.description ; The exposure time in micro-seconds ; _item.name '_em_micrographs.exposure_time' _item.category_id em_micrographs _item.mandatory_code no _item_type.code float save_ save__em_micrographs.exposure_type _item_description.description ; The exposure type ; _item.name '_em_micrographs.exposure_type' _item.category_id em_micrographs _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value normal dark save_ ########################## ## EM_MICROSCOPE ## ########################## save_em_microscope _category.description ; Data items in the EM_MICROSCOPE category record details about the microscope ; _category.id em_microscope _category.mandatory_code no _category_key.name '_em_microscope.id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_data_collection_group' save_ save__em_microscope.id _item_description.description ; The value of _em_microscope.id must uniquely identify a microscope used in the em experiments. ; _item.name '_em_microscope.id' _item.category_id em_microscope _item.mandatory_code yes _item_type.code code save_ save__em_microscope.model _item_description.description ; The microscope model ; _item.name '_em_microscope.model' _item.category_id em_microscope _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value 'HITACHI H8100' 'HITACHI HF2000' 'HITACHI HF2000-UHR' 'HITACHI H9000-UHR' 'HITACHI H9000-NAR' 'HITACHI 300KEV FEG' 'HITACHI HU1250' 'HITACHI H-1500' 'JEOL 2000EX' 'JEOL 2010HT' 'JEOL 2010UHR' 'JEOL 2010F' 'JEOL 3010HT' 'JEOL 3010UHR' 'JEOL KYOTO-3000SFF' 'JEOL 4000EX' 'JEOL HAREM' 'JEOL ARM-1000' 'FEI/PHILIPS CM120T' 'FEI/PHILIPS CM200T' 'FEI/PHILIPS CM20/ST' 'FEI/PHILIPS CM20/SOPHIE' 'FEI/PHILIPS CM200FEG/ST' 'FEI/PHILIPS CM20/UT' 'FEI/PHILIPS CM200FEG/UT' 'FEI/PHILIPS CM30/T' 'FEI/PHILIPS CM300FEG/T' 'FEI/PHILIPS CM300FEG/HE' 'FEI/PHILIPS CM30/ST' 'FEI/PHILIPS CM300FEG/ST' 'FEI/PHILIPS CM300FEG/UT' 'FEI TECNAI 12' 'FEI TECNAI 20' 'FEI TECNAI F20' 'FEI TECNAI F30' 'FEI MORGAGNI' 'JEOL 1200' 'JEOL 1210' 'JEOL 1010' 'JEOL 2500SE' 'JEOL 1230' 'JEOL ARM1300' 'JEOL 4010' 'JEOL 2010' 'JEOL 3000F' 'JEOL 3010' 'JEOL 3010F' 'JEOL 3100' 'JEOL 3200FS' 'JEOL 2200FS' 'JEOL 2100' 'JEOL 2100F' 'FEI TECNAI SPHERA' 'FEI TECNAI POLORA' 'FEI TECNAI 30' 'FEI TECNAI SPIRIT TWIN' 'FEI TECNAI SPIRIT BIOTWIN' 'ZEISS LIBRA EFTEM 120' 'ZEISS LIBRA EFTEM 200FE' save_ save__em_microscope.electron_source _item_description.description ; The source of electrons. The electron gun. ; _item.name '_em_microscope.electron_source' _item.category_id em_microscope _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value 'FIELD EMISSION GUN' LAB6 'TUNGSTEN HAIRPIN' OTHER save_ save__em_microscope.nominal_cs _item_description.description ; The spherical aberration coefficient (Cs) in millimetres, of the objective lens. ; _item.name '_em_microscope.nominal_cs' _item.category_id em_microscope _item.mandatory_code no _item_type.code float _item_units.code millimetres _item_examples.case 1.4 save_ ################# ## EM_CLASSES ## ################# save_em_classes _category.description ; Data items in the EM_CLASSES category record details about the particle classification. Particle classification involves grouping images that are similar, and separating images that are distinct. In practical use, this means that experimental projections that have the same orientation (shape) are placed within the same category for later averaging. In this case, orientation means that the particles are showing the same face to the viewer and the only difference between them is that they can be rotated by some angle in the plane of the image. The experimental projections might also be shifted relative to each other, but the centering of the experimental projections is often done before classification. is this required? E(e1,e2,e3) = E(w,h,i) cos(i)cos(h)cos(w)-sin(i)sin(h) cos(i)cos(h)sin(w)+sin(i)sin(h) -cos(i)sin(h) -sin(i)cos(h)cos(w)-cos(i)sin(h) sin(i)cos(h)sin(w)+cos(i)sin(h) sin(i)sin(h) sin(h)cos(w) sin(h)sin(w) cos(h) ; _category.id em_classes _category.mandatory_code no _category_key.name '_em_classes.id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_reconstruction_group' 'em_single_particle_group' save_ save__em_classes.id _item_description.description ; The value of _em_classes.id must uniquely identify the classes used in the em experiments. ; _item.name '_em_classes.id' _item.category_id em_classes _item.mandatory_code yes _item_type.code code save_ save__em_classes.details _item_description.description ; Description of the classes derived in the em experiments. ; _item.name '_em_classes.details' _item.category_id em_classes _item.mandatory_code no _item_type.code text loop_ _item_examples.case _item_examples.detail 1 ; We have used size variation analyses to classify images recorded from preparations of the WT S. cerevisiae PDC to which sufficient E1 was added to occupy its 60 binding sites and the same preparation with about one-third of the E1 binding sites occupied. Two 3D reconstructions representative of images that vary in size by 10-12% (~50 Angstroms in diameter) from these preparations were computed to document the E1 organization about the core and the length of its inner linkers. In this regard, our previous structure of the WT bovine kidney PDC in which ~22 E1s were bound indicated that the outer shell could readily accommodate 60 molecules of E1 without significant crowding. Surprisingly, this study shows that extensive E1 binding favors a more extended inner linker and an altered arrangement of E1 about the core. ; 2 ; The focal pair method of orientation determination, refinement, and 3D reconstruction as implemented in the IMIRS software package was used except that an additional step of particle-size evaluation was performed in the current reconstruction. Data sets consisting of 1,500 and 690 particle images of PDC with a molar ratio of 60 E1/E2 core and ~24 E1/E2 core, respectively, were processed. For both data sets, an iterative procedure was implemented to classify the particles according to their sizes by using the SIZEDIFF program with contrast transfer function correction incorporated. A preliminary 3D reconstruction was calculated by combining all of the particles, and this "average" reconstruction was used to classify the images into a 1.0 size group comprising a 3% size variation of the images. For the PDC with ~60 E1/E2 core, the converged structure from 128 images in the 1.0 size group, was then used as a model to classify 45 and 80 images in the 0.95 and 1.05 size groups, respectively. For the WT PDC preparation (24 E1/E2 core) the converged structure from 80 images in the 1.0 size group was used as model to classify 46 and 53 images in the 0.95 and 1.05 size groups, respectively. The image size distribution appears bell-shaped and is consistent with a more extensive data set of the human PDC (Y.G., Z.H.Z., Y. Hiromasa, H. Bao, X. Yan, T. E. Roche, and J.K.S., unpublished results). The finding that 1.0 size groups consist of the larger and smaller reconstructions in the PDC preparations according to their greater or lesser degree of E1 occupancy, respectively, indicates that the extent of E1 binding is related to the variable size of the molecules. ; 3 ; A classification was performed using the self-organizing map (SOM) algorithms of the XMIPP package. The entire set was first low pass-filtered to 3.2 nm, and a reference-free alignment was performed using the Spider software package. Transformations in x, y, and in-plane angle were imposed, and the data set was fed to the kernel density SOM procedure using a 10 x 10 grid. The procedure generates a grid of code vectors that represent the assigned images. It was verified that clean looking code vectors represented classes of clean particles, while particles assigned to defect-ridden code vectors were themselves of poor quality. The procedure was repeated several times with different parameters, and in each case a set of roughly 3000 good particles was obtained. Further processing was conducted on a set containing 2943 particles. ; 4 ; The picked particles were submitted to a multivariate statistical analysis without alignment and were classified into clusters of particles with similar features. To this end, a program package kindly provided by J. P. Bretaudiere was used. The various cluster averages revealed square and round shaped particles at different angular orientations. These averages were taken as references for subsequent angular and translational alignment of the extracted 4096 particles. Aligned particles were classified again, and cluster averages were calculated. ; save_ save__em_classes.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_classes.entry_id' _item.category_id em_classes _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_classes.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_classes.origin_x _item_description.description ; The class origin in X ; _item.name '_em_classes.origin_x' _item.category_id em_classes _item.mandatory_code no _item_type.code float save_ save__em_classes.origin_y _item_description.description ; The class origin in Y ; _item.name '_em_classes.origin_y' _item.category_id em_classes _item.mandatory_code no _item_type.code float save_ save__em_classes.euler_1 _item_description.description ; The euler angle about z-axis ; _item.name '_em_classes.euler_1' _item.category_id em_classes _item.mandatory_code no _item_type.code float save_ save__em_classes.euler_2 _item_description.description ; The euler angle about y-axis ; _item.name '_em_classes.euler_2' _item.category_id em_classes _item.mandatory_code no _item_type.code float save_ save__em_classes.euler_3 _item_description.description ; The second euler angle about z-axis ; _item.name '_em_classes.euler_3' _item.category_id em_classes _item.mandatory_code no _item_type.code float save_ save__em_classes.num_particles _item_description.description ; The number of particles used in the class average ; _item.name '_em_classes.num_particles' _item.category_id em_classes _item.mandatory_code no _item_type.code int save_ save__em_classes.angular_error_threshold _item_description.description ; The percentage angular error threshold ; _item.name '_em_classes.angular_error_threshold' _item.category_id em_classes _item.mandatory_code no _item_type.code float save_ save__em_classes.internal_resolution_flag _item_description.description ; flag for method used for internal resolution ; _item.name '_em_classes.internal_resolution_flag' _item.category_id em_classes _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail O OTHER S 'S image' I 'I image' save_ save__em_classes.average_angular_error _item_description.description ; The average_angular_error in degrees ; _item.name '_em_classes.average_angular_error' _item.category_id em_classes _item.mandatory_code no _item_type.code float save_ save__em_classes.average_translational_pixel_shift_error _item_description.description ; The average_translational_pixel_shift_error ; _item.name '_em_classes.average_translational_pixel_shift_error' _item.category_id em_classes _item.mandatory_code no _item_type.code float save_ save__em_classes.fractional_minimum_amplitude _item_description.description ; The fractional_minimum_amplitude ; _item.name '_em_classes.fractional_minimum_amplitude' _item.category_id em_classes _item.mandatory_code no _item_type.code float save_ save__em_classes.global_correlation_coefficient _item_description.description ; The global_correlation_coefficient ; _item.name '_em_classes.global_correlation_coefficient' _item.category_id em_classes _item.mandatory_code no _item_type.code float save_ save__em_classes.global_real-space_correlation_coefficient _item_description.description ; The global_real-space_correlation_coefficient ; _item.name '_em_classes.global_real-space_correlation_coefficient' _item.category_id em_classes _item.mandatory_code no _item_type.code float save_ save__em_classes.clustering_method _item_description.description ; The clustering_method used ; _item.name '_em_classes.clustering_method' _item.category_id em_classes _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail 'single linkage' . 'complete linkage' . 'average linkage' . 'centroid method' . 'Wards method' . 'Correspondence Analysis' ; (CA) uses Chi-squared distance This is superior because it ignores differences in exposure between images, eliminating the need to rescale between images. ; 'Principal Component Analysis' ; (PCA) computes the distance between data vectors with Euclidean distances. ; 'Didays method' ; A disadvantage of the K-means method is that the final grouping is very dependent of what seeds are initially chosen. Diday surpassed this by appplying the K-means technique multiple times with different seeds. Then, cross-tabuluating the results, and using only the clusters that were repeatedly formed. ; 'Automatic Clustering and Hierarchical Ascendant Classifications (HAC)' ; HAC it uses only Ward's criterion. Ward's criterion states that merging HAC clusters should be focused on minimizing the added interclass variance. The two clusters that differ the least between each other will be merged and create a new group, one "level" higher. ; 'K-Means Clustering' ; K-Means is a method of clustering that devides the data into a user defined number of groups. Two random images "seeds" are chosen, and their centers of gravity are computed. A partition is drawn down the middle between the centers, the new centers of gravity are computed, and the process is repeated for a given number of times. The final result is VERY dependent on which image seeds are the first chosen. Because our faces data set is manufactured. We know exactly which images are identical, except the random noise, and the exact number of groups. The output discussed was obtained with 8 classes, using factors 1-3, and an even factor weight of 1.0 between those three factors. ; save_ save__em_classes.alignment_method _item_description.description ; The alignment_method used ; _item.name '_em_classes.alignment_method' _item.category_id em_classes _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail 'Reference-based alignment' ; We assume that the reference image is known or that a good approximation of it is available. We expect all the particles to be noisy versions of the reference, with possible small variations. In this case the alignment problem becomes a pattern matching problem. We have to place every particle in an orientation in which it will best match the reference image. In the case of many reference images, in addition, we have to decide which reference is the most similar one. We must also try the mirror orientation since the particle may be flipped. ; 'Alignment with the reference refinement' ; We assume that a set of particles in one orientation is available. Particles are not identical, but they share the same motif. begins with calculation of the global average to approximate the reference, then aligns all the images and calculates new average to obtain improved reference. These steps are iterated prescribed number of times. ; 'Multireference alignment' ; We assume that a very large data set is available. It comprises particles in a few distinct orientations. The data set is sufficiently large that at least some of the similar views occur in similar in-plane orientations, and so can be averaged. Thus, if we can approximately center the particles, the subsequent classification step should reveal some of the classes. These classes are used as reference images in the next multireference alignment step, classification is repeated, and new classes are formed. This procedure is iterated until stable classes are obtained. Such a multireference alignment is sometimes called alignment through classification. This name reflects the idea that alignment is done separately within groups produced by the classification step. (a) - radius for alignment and mask -- should correspond to the particle radius; (b) - whether classification is done using all pixels within mask in the computation of Euclidean distance, or factors from Principal Component Analysis (PCA); (c) - if PCA is to be used, the number of factors has to be set; (d) - the number of groups into which the data set will be divided -- this determines the number of class averages that will be obtained; (e) - the number of times the procedure should be repeated. ; 'Reference-free alignment' ; The reference-free alignment Will seek such orientations of all the particles in the data set that all the possible pairs of images from this set are in the 'best' relative orientation as determined by the maximum of the CCF. The reference-free alignment programs were designed for very noisy data, for particles in many different orientations, and in general for cases in which a reference image is unknown or in which its usage could result in a bias and incorrect results. ; save_ ####################### ## EM_3D_REFINEMENT ## ####################### save_em_3d_refinement _category.description ; Data items in the EM_3D_REFINEMENT category record details about the class/particle refinement. In random conical tilt, images were assigned angular positions through rotational alignment and tilt-angles. From each different class, a three-dimensional preliminary model is constructed. To improve the output, those preliminary models from each class that have a high degree of similarity are merged. In theory, these models corresponded to groups of the same molecule just viewed from different orientations. Once all the good random conical tilt models (and their corresponding particle data sets) have been merged, iterative angular refinement is used to improve the model's resolution. Equidistant projections are first generated from the merged model. The entire particle data set (whether the old random conical tilt experimental particles, or new untilted experimental particles, or both) is then cross correlated to each reference projection. A correlation coefficient is generated between each experimental particle and reference projection. For each individual experimental particle, it is matched to the reference projection that gave the highest correlation coefficient. Therefore, it is assumed that this particle matches the Euler angles of the reference projection. ; _category.id em_3d_refinement _category.mandatory_code no _category_key.name '_em_3d_refinement.id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_reconstruction_group' 'em_single_particle_group' save_ save__em_3d_refinement.id _item_description.description ; The value of _em_3d_refinement.id must uniquely identify the refinement used in the em experiments. ; _item.name '_em_3d_refinement.id' _item.category_id em_3d_refinement _item.mandatory_code yes _item_type.code code save_ save__em_3d_refinement.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_3d_refinement.entry_id' _item.category_id em_3d_refinement _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_3d_refinement.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_3d_refinement.method_details _item_description.description ; Description of the 3d refinement method ; _item.name '_em_3d_refinement.method_details' _item.category_id em_3d_refinement _item.mandatory_code no _item_type.code text save_ save__em_3d_refinement.num_iterations _item_description.description ; the number of iterations used in refinement ; _item.name '_em_3d_refinement.num_iterations' _item.category_id em_3d_refinement _item.mandatory_code no _item_type.code int save_ save__em_3d_refinement.angular_search_step_size _item_description.description ; the angular_search_step_size used in refinement ; _item.name '_em_3d_refinement.angular_search_step_size' _item.category_id em_3d_refinement _item.mandatory_code no _item_type.code float save_ save__em_3d_refinement.max_spatial_frequency _item_description.description ; the max_spatial_frequency used in refinement (1/A) ; _item.name '_em_3d_refinement.max_spatial_frequency' _item.category_id em_3d_refinement _item.mandatory_code no _item_type.code float save_ save__em_3d_refinement.max_spatial_frequency_criterion _item_description.description ; The criterion used to determine the maximum spatial frequency. ; _item.name '_em_3d_refinement.max_spatial_frequency_criterion' _item.category_id em_3d_refinement _item.mandatory_code no _item_type.code text save_ save__em_3d_refinement.structure_radius _item_description.description ; the structure_radius in pixels ; _item.name '_em_3d_refinement.structure_radius' _item.category_id em_3d_refinement _item.mandatory_code no _item_type.code float save_ save__em_3d_refinement.projection_radius _item_description.description ; the Projection radius in pixels ; _item.name '_em_3d_refinement.projection_radius' _item.category_id em_3d_refinement _item.mandatory_code no _item_type.code float save_ save__em_3d_refinement.alignment_radius _item_description.description ; Alignment radius (pixels) used in alignment search ; _item.name '_em_3d_refinement.alignment_radius' _item.category_id em_3d_refinement _item.mandatory_code no _item_type.code float save_ save__em_3d_refinement.convergence_criterion _item_description.description ; Convergence criterion fraction e.g. Converges when x16 % of all images move < 1.5 * stepsize ; _item.name '_em_3d_refinement.convergence_criterion' _item.category_id em_3d_refinement _item.mandatory_code no _item_type.code text save_ save__em_3d_refinement.num_particles_refined _item_description.description ; The number of particles used in refinement. ; _item.name '_em_3d_refinement.num_particles_refined' _item.category_id em_3d_refinement _item.mandatory_code no _item_type.code int save_ ####################### # EM_MAP_RESOLUTION # ####################### save_em_map_resolution _category.description ; Data items in the EM_MAP_RESOLUTION category record details about the Fourier Shell Correlation The most popular method at the moment for resolution assessment is the Fourier Shell Correlation, although there is no standard way to define the cutoff value. It assumes a uniform distribution of the resolution along the three-dimensions (so there is a single value of resolution). The Fourier Shell Correlation curve is defined as a list of value pairs (x, y) where x is the spatial frequency (or inverse resolution in 1/A) and y is the correlation coefficient (a value between 0 and 1). ; _category.id em_map_resolution _category.mandatory_code no _category_key.name '_em_map_resolution.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_map_group' loop_ _category_examples.detail _category_examples.case ; Example 1 ; ; _em_map_resolution.entry_id EM9999 _em_map_resolution.title "ACh receptor FSC Plot" _em_map_resolution.x_axis "Resolution (A-1)" _em_map_resolution.y_axis "Correlation Coefficient" ; save_ save__em_map_resolution.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_map_resolution.entry_id' _item.category_id em_map_resolution _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_map_resolution.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_map_resolution.title _item_description.description ; The title of the FSC graph - equivalent to the name of the assembly of observed complexes. ; _item.name '_em_map_resolution.title' _item.category_id em_map_resolution _item.mandatory_code yes _item_type.code line save_ save__em_map_resolution.x_axis _item_description.description ; The title of the x_axis in the FSC graph Usually the resolution in reciprical Angstroms may be spatial_frequency ; _item.name '_em_map_resolution.x_axis' _item.category_id em_map_resolution _item.mandatory_code yes _item_type.code line save_ save__em_map_resolution.y_axis _item_description.description ; The title of the y_axis in the FSC graph The Correlation coefficient or sigma_value ; _item.name '_em_map_resolution.y_axis' _item.category_id em_map_resolution _item.mandatory_code yes _item_type.code line save_ save__em_map_resolution.map_id _item_description.description ; _em_map_resolution.map_id is a pointer to _em_map.id in the EM_MAP category ; _item.name '_em_map_resolution.map_id' _item.category_id em_map_resolution _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_map_resolution.map_id' _item_linked.parent_name '_em_map.id' save_ save__em_map_resolution.curve_id _item_description.description ; _em_map_resolution.curve_id uniquely identifies a fsc plot ; _item.name '_em_map_resolution.curve_id' _item.category_id em_map_resolution _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_map_resolution.curve_id' _item_linked.parent_name '_em_fsc_curve.curve_id' save_ save__em_map_resolution.cutoff_used _item_description.description ; The cutoff value to estimate the resolution value can be defined by: - the point of the curve where the correlation is 0.5 - the point of the curve that crosses a significance threshold curve According to Orlova et al. 1997 (J Mol Biol, 271:417) this significance threshold curve is defined as the 3*sigma (sigma = standard deviation of the FSC) for non-symmetrical particles. (units: 1/A) [stc stands for significance threshold curve] ; _item.name '_em_map_resolution.cutoff_used' _item.category_id em_map_resolution _item.mandatory_code no _item_type.code float save_ save__em_map_resolution.sigma_weight _item_description.description ; the curve has to be weigthed taking into the account the number of independent asymmetric units (N). In that case the curve would be defined as sqrt(N)*3*sigma. This is the weighted factor used. If this weighted factor is always defined as 3*sqrt(N) then we only need to know the number of independent units N. ; _item.name '_em_map_resolution.sigma_weight' _item.category_id em_map_resolution _item.mandatory_code no _item_type.code float save_ save__em_map_resolution.fsc_criteria _item_description.description ; The value of the fourier shell correlation criterion. A more accurate measure of the resolution is obtained by multiplying the sigma threshold value by the square root of the number of asymmetric units within the given point group symmetry. Reference: (Orlova et al, J mol Biol, 271, 417-437,1997). ; _item.name '_em_map_resolution.fsc_criteria' _item.category_id em_map_resolution _item.mandatory_code no _item_type.code float save_ save__em_map_resolution.3d_reconstruction_resolution_method _item_description.description ; Method used to determine the resolution of the map. The first of the two fundamentally different methods is one that relies on dividing the the data into two halves and then calculating two independent reconstructions which are then compared by Fourier Shell Correlation (FSC) or differential phase residual (DPR). The second different method of assessing resolution is more relevant where there is a combination of EM and X-ray data. The similarity between the EM density and the electron density corresponding to the atomic structure can be used to determine the resolution of the EM map. ; _item.name '_em_map_resolution.3d_reconstruction_resolution_method' _item.category_id em_map_resolution _item.mandatory_code no _item_type.code text save_ save__em_map_resolution.resolution_cut_off_criteria _item_description.description ; The cut-off criteria used in the resolution determination.e.g an FSC limit of 0.5 is used as a conservative measure of resolution. ; _item.name '_em_map_resolution.resolution_cut_off_criteria' _item.category_id em_map_resolution _item.mandatory_code no _item_type.code line save_ save__em_map_resolution.nyquist_frequency _item_description.description ; The Nyquist frequency is double the sampling step. e.g. for data sampled at 5 angstroms the Nyquist frequency is 1/10 angstroms. It is important to have the sampling rate of the data high enough so that the image information stays sufficiently away from the Nyquist frequency, otherwise there is a danger that the high- resolution information in both of the reconstruction volumes may be correlated. ; _item.name '_em_map_resolution.nyquist_frequency' _item.category_id em_map_resolution _item.mandatory_code no _item_type.code float save_ save__em_map_resolution.fsc_significance_threshold _item_description.description ; The fourier shell correlation significance threshold in sigma. e.g. a 3 sigma threshold is three standard deviations over the random noise value. ; _item.name '_em_map_resolution.fsc_significance_threshold' _item.category_id em_map_resolution _item.mandatory_code no _item_type.code float save_ save__em_map_resolution.fsc_spatial_frequency _item_description.description ; The fourier shell correlation spatial frequency value. ; _item.name '_em_map_resolution.fsc_spatial_frequency' _item.category_id em_map_resolution _item.mandatory_code no _item_type.code float save_ save__em_map_resolution.spectral_value _item_description.description ; The spectral-signal-to-noise ratio value. This two-dimensional resolution determination method compares reprojections. ; _item.name '_em_map_resolution.spectral_value' _item.category_id em_map_resolution _item.mandatory_code no _item_type.code float save_ save__em_map_resolution.dpr_spatial_frequency _item_description.description ; The two dimensional differential phase residual spatial frequency value. ; _item.name '_em_map_resolution.dpr_spatial_frequency' _item.category_id em_map_resolution _item.mandatory_code no _item_type.code float save_ save__em_map_resolution.dpr_value _item_description.description ; The differential phase residual value. ; _item.name '_em_map_resolution.dpr_value' _item.category_id em_map_resolution _item.mandatory_code no _item_type.code float save_ save__em_map_resolution.dpr_crit _item_description.description ; The value of the differential phase residual criterion. ; _item.name '_em_map_resolution.dpr_crit' _item.category_id em_map_resolution _item.mandatory_code no _item_type.code float save_ save__em_map_resolution.details _item_description.description ; Any additional details about the resolution determination method. ; _item.name '_em_map_resolution.details' _item.category_id em_map_resolution _item.mandatory_code no _item_type.code text save_ ################## # EM_FSC_CURVE # ################## save_em_fsc_curve _category.description ; Data items in the EM_FSC_CURVE category record the values for the Fourier Shell Correlation Curve ; _category.id em_fsc_curve _category.mandatory_code no loop_ _category_key.name '_em_fsc_curve.id' '_em_fsc_curve.curve_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_map_group' save_ save__em_fsc_curve.curve_id _item_description.description ; _em_fsc.curve_id uniquely identifies a fsc plot and is a pointer to _em_fsc.curve_id in the EM_FSC category ; _item.name '_em_fsc_curve.curve_id' _item.category_id em_fsc_curve _item.mandatory_code yes _item_type.code code save_ save__em_fsc_curve.id _item_description.description ; This data item uniquely identifies a row in the FSC curve ; _item.name '_em_fsc_curve.id' _item.category_id em_fsc_curve _item.mandatory_code yes _item_type.code int save_ save__em_fsc_curve.x _item_description.description ; The x values in the FSC curve ; _item.name '_em_fsc_curve.x' _item.category_id em_fsc_curve _item.mandatory_code yes _item_type.code float save_ save__em_fsc_curve.y _item_description.description ; The y values in the FSC curve ; _item.name '_em_fsc_curve.y' _item.category_id em_fsc_curve _item.mandatory_code yes _item_type.code float save_ ############## # EM_STAIN # ############## save_em_stain _category.description ; Data items in the EM_STAIN category record details about the staining techniques used. ; _category.id em_stain _category.mandatory_code yes loop_ _category_key.name '_em_stain.id' '_em_stain.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_specimen_preparation_group' save_ save__em_stain.id _item_description.description ; The value of _em_stain.id must uniquely identify set of stain parameters ; _item.name '_em_stain.id' _item.category_id em_stain _item.mandatory_code yes _item_type.code code save_ save__em_stain.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_stain.entry_id' _item.category_id em_stain _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_stain.entry_id' _item_linked.parent_name '_entry.id' save_ #save__em_stain.cryo_flag # _item_description.description #; A mandatory flag to indicate if the data items # describe cryo staining or not #; # _item.name '_em_stain.cryo_flag' # _item.category_id em_stain # _item.mandatory_code yes # _item_type.code line # loop_ # _item_enumeration.value # YES # NO # save_ save__em_stain.details _item_description.description ; General details on the staining techniques used ; _item.name '_em_stain.details' _item.category_id em_stain _item.mandatory_code no _item_type.code text save_ save__em_stain.citation _item_description.description ; Text describing a reference citation on the staining techniques used ; _item.name '_em_stain.citation' _item.category_id em_stain _item.mandatory_code no _item_type.code text save_ save__em_stain.protocol _item_description.description ; Text describing the protocol for the staining techniques used ; _item.name '_em_stain.protocol' _item.category_id em_stain _item.mandatory_code no _item_type.code text save_ save__em_stain.time_resolved_state _item_description.description ; Text giving details on the time factors involved in the staining techniques used ; _item.name '_em_stain.time_resolved_state' _item.category_id em_stain _item.mandatory_code no _item_type.code text save_ #save__em_stain.cryogen_name # _item_description.description #; If the details given are for a cryogen staining # method the name of the cryogen used #; # _item.name '_em_stain.cryogen_name' # _item.category_id em_stain # _item.mandatory_code no # _item_type.code text # save_ save__em_stain.temperature _item_description.description ; The staining technique temperature used ; _item.name '_em_stain.temperature' _item.category_id em_stain _item.mandatory_code no _item_type.code text save_ save__em_stain.humidity _item_description.description ; The humidity at which the staining technique was used ; _item.name '_em_stain.humidity' _item.category_id em_stain _item.mandatory_code no _item_type.code text save_ save__em_stain.type _item_description.description ; The general class or type of the staining technique used ; _item.name '_em_stain.type' _item.category_id em_stain _item.mandatory_code no _item_type.code text save_ #save__em_stain.instrument # _item_description.description #; Details on the instrument used in the staining technique # used #; # _item.name '_em_stain.instrument' # _item.category_id em_stain # _item.mandatory_code no # _item_type.code text # save_ # save__em_stain.sample_preparation_id _item_description.description ; A pointer to _em_sample_preparation.id in the EM_SAMPLE_PREPARATION category ; _item.name '_em_stain.sample_preparation_id' _item.category_id em_stain _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_stain.sample_preparation_id' _item_linked.parent_name '_em_sample_preparation.id' save_ ################### # EM_CRYO_STAIN # ################### save_em_cryo_stain _category.description ; Data items in the EM_CRYO_STAIN category record details about the staining techniques used. ; _category.id em_cryo_stain _category.mandatory_code yes loop_ _category_key.name '_em_cryo_stain.id' '_em_cryo_stain.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_specimen_preparation_group' save_ save__em_cryo_stain.id _item_description.description ; The value of _em_cryo_stain.id must uniquely identify set of stain parameters ; _item.name '_em_cryo_stain.id' _item.category_id em_cryo_stain _item.mandatory_code yes _item_type.code code save_ save__em_cryo_stain.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_cryo_stain.entry_id' _item.category_id em_cryo_stain _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_cryo_stain.entry_id' _item_linked.parent_name '_entry.id' save_ #save__em_cryo_stain.cryo_flag # _item_description.description #; A mandatory flag to indicate if the data items # describe cryo staining or not #; # _item.name '_em_cryo_stain.cryo_flag' # _item.category_id em_cryo_stain # _item.mandatory_code yes # _item_type.code line # loop_ # _item_enumeration.value # YES # NO # save_ save__em_cryo_stain.details _item_description.description ; General details on the staining techniques used ; _item.name '_em_cryo_stain.details' _item.category_id em_cryo_stain _item.mandatory_code no _item_type.code text save_ save__em_cryo_stain.citation _item_description.description ; Text describing a reference citation on the staining techniques used ; _item.name '_em_cryo_stain.citation' _item.category_id em_cryo_stain _item.mandatory_code no _item_type.code text save_ save__em_cryo_stain.protocol _item_description.description ; Text describing the protocol for the staining techniques used ; _item.name '_em_cryo_stain.protocol' _item.category_id em_cryo_stain _item.mandatory_code no _item_type.code text save_ save__em_cryo_stain.time_resolved_state _item_description.description ; Text giving details on the time factors involved in the staining techniques used ; _item.name '_em_cryo_stain.time_resolved_state' _item.category_id em_cryo_stain _item.mandatory_code no _item_type.code text save_ save__em_cryo_stain.cryogen_name _item_description.description ; If the details given are for a cryogen staining method the name of the cryogen used ; _item.name '_em_cryo_stain.cryogen_name' _item.category_id em_cryo_stain _item.mandatory_code no _item_type.code text save_ save__em_cryo_stain.temperature _item_description.description ; The staining technique temperature used ; _item.name '_em_cryo_stain.temperature' _item.category_id em_cryo_stain _item.mandatory_code no _item_type.code text save_ save__em_cryo_stain.humidity _item_description.description ; The humidity at which the staining technique was used ; _item.name '_em_cryo_stain.humidity' _item.category_id em_cryo_stain _item.mandatory_code no _item_type.code text save_ save__em_cryo_stain.type _item_description.description ; The general class or type of the staining technique used ; _item.name '_em_cryo_stain.type' _item.category_id em_cryo_stain _item.mandatory_code no _item_type.code text save_ save__em_cryo_stain.instrument _item_description.description ; Details on the instrument used in the staining technique used ; _item.name '_em_cryo_stain.instrument' _item.category_id em_cryo_stain _item.mandatory_code no _item_type.code text save_ save__em_cryo_stain.sample_preparation_id _item_description.description ; A pointer to _em_sample_preparation.id in the EM_SAMPLE_PREPARATION category ; _item.name '_em_cryo_stain.sample_preparation_id' _item.category_id em_cryo_stain _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_cryo_stain.sample_preparation_id' _item_linked.parent_name '_em_sample_preparation.id' save_ ######################## # EM_EMBEDDING_AGENT # ######################## save_em_embedding_agent _category.description ; Data items in the EM_EMBEDDING_AGENT category record details about the type of reagents into which the sample was embedded ; _category.id em_embedding_agent _category.mandatory_code yes loop_ _category_key.name '_em_embedding_agent.id' '_em_embedding_agent.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_specimen_preparation_group' save_ save__em_embedding_agent.id _item_description.description ; The value of _em_embedding_agent.id must uniquely identify set of the embedding agent parameters ; _item.name '_em_embedding_agent.id' _item.category_id em_embedding_agent _item.mandatory_code yes _item_type.code code save_ save__em_embedding_agent.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_embedding_agent.entry_id' _item.category_id em_embedding_agent _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_embedding_agent.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_embedding_agent.type _item_description.description ; The type of embedding agent used ; _item.name '_em_embedding_agent.type' _item.category_id em_embedding_agent _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value glucose trehalose glycerol sucrose "tannic acid" other save_ save__em_embedding_agent.details _item_description.description ; General details on the embedding agent used ; _item.name '_em_embedding_agent.details' _item.category_id em_embedding_agent _item.mandatory_code no _item_type.code text save_ save__em_embedding_agent.citation _item_description.description ; Details on a reference citation on the embedding agent used ; _item.name '_em_embedding_agent.citation' _item.category_id em_embedding_agent _item.mandatory_code no _item_type.code text save_ save__em_embedding_agent.temperature _item_description.description ; The temperature the embedding agent was used at ; _item.name '_em_embedding_agent.temperature' _item.category_id em_embedding_agent _item.mandatory_code no _item_type.code float save_ save__em_embedding_agent.time_resolved _item_description.description ; Details about the effect of time resolution for the embedding agent used ; _item.name '_em_embedding_agent.time_resolved' _item.category_id em_embedding_agent _item.mandatory_code no _item_type.code line save_ ############## ## EM_MAP ## ############## save_em_map _category.description ; Data items in the EM_MAP category record details about the type of the 3d-em map. The map is represented logically as a three-dimensional array of data-values of the same data-type. To interpret the contents of of a 3d-map file it is necessary to know the data-type of the array and the size of the array in three dimensions (i.e.the number of columns, rows and sections). In a 1d-array representation columns are the fastest changing, followed by rows and sections. The first element of the array will have index 0. The 3d-em map is in a defined orientation/position in Universal 3D Space. This space is described by a right-handed cartesian coordinate system (and is the same coordinate system as that used for structures deposited in the PDB). ; _category.id em_map _category.mandatory_code yes loop_ _category_key.name '_em_map.id' '_em_map.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_map_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_map.id 1 _em_map.pdb_entry_id 1DYL _em_map.entry_id EM9999 _em_map.num_columns 100 _em_map.num_rows 100 _em_map.num_sections 100 _em_map.num_spacing_x 2.0 _em_map.num_spacing_y 2.0 _em_map.num_spacing_z 2.0 _em_map.details . _em_map.value_density_max . _em_map.value_density_min . _em_map.value_density_mean . ; save_ save__em_map.3d_reconstruction_id _item_description.description ; This data item is a pointer to the 3D_RECONSTRUCTION category. ; _item.name '_em_map.3d_reconstruction_id' _item.category_id em_map _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_map.3d_reconstruction_id' _item_linked.parent_name '_em_3d_reconstruction.id' save_ save__em_map.imaging_id _item_description.description ; This data item is a pointer to the IMAGING category. ; _item.name '_em_map.imaging_id' _item.category_id em_map _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_map.imaging_id' _item_linked.parent_name '_em_imaging.id' save_ save__em_map.entry_id _item_description.description ; This data item is a pointer to the ENTRY category. ; _item.name '_em_map.entry_id' _item.category_id em_map _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_map.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_map.map_files_id _item_description.description ; This data item is a pointer to the MAP_FILES category. ; _item.name '_em_map.map_files_id' _item.category_id em_map _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_map.map_files_id' _item_linked.parent_name '_em_map_files.id' save_ save__em_map.num_columns _item_description.description ; The number of columns of the map. ; _item.name '_em_map.num_columns' _item.category_id em_map _item.mandatory_code yes _item_type.code int save_ save__em_map.num_rows _item_description.description ; The number of rows of the map. ; _item.name '_em_map.num_rows' _item.category_id em_map _item.mandatory_code yes _item_type.code int save_ save__em_map.num_sections _item_description.description ; The number of sections of the map. ; _item.name '_em_map.num_sections' _item.category_id em_map _item.mandatory_code yes _item_type.code int save_ save__em_map.spacing_x _item_description.description ; The length of the x interval in microns. ; _item.name '_em_map.spacing_x' _item.category_id em_map _item.mandatory_code yes _item_type.code float save_ save__em_map.spacing_y _item_description.description ; The length of the y interval in microns. ; _item.name '_em_map.spacing_y' _item.category_id em_map _item.mandatory_code yes _item_type.code float save_ save__em_map.spacing_z _item_description.description ; The length of the z interval in microns. ; _item.name '_em_map.spacing_z' _item.category_id em_map _item.mandatory_code yes _item_type.code float save_ save__em_map.data_type _item_description.description ; The map data_type describes the types of data in the map. Mode defines the data structure on disc. Mode 0=integer*1;mode 1=integer*2;mode 2=real*4. Mode 2 is the normal mode used in CCP4 programs. ; _item.name '_em_map.data_type' _item.category_id em_map _item.mandatory_code yes _item_type.code int save_ save__em_map.pixel_x _item_description.description ; The x pixel size ; _item.name '_em_map.pixel_x' _item.category_id em_map _item.mandatory_code no _item_type.code float save_ save__em_map.pixel_y _item_description.description ; The y pixel size ; _item.name '_em_map.pixel_y' _item.category_id em_map _item.mandatory_code no _item_type.code float save_ save__em_map.pixel_z _item_description.description ; The z pixel size ; _item.name '_em_map.pixel_z' _item.category_id em_map _item.mandatory_code no _item_type.code float save_ save__em_map.row_limit _item_description.description ; The limit in row size ; _item.name '_em_map.row_limit' _item.category_id em_map _item.mandatory_code no _item_type.code float save_ save__em_map.col_limit _item_description.description ; The limit in column size ; _item.name '_em_map.col_limit' _item.category_id em_map _item.mandatory_code no _item_type.code float save_ save__em_map.sec_limit _item_description.description ; The limit in section size ; _item.name '_em_map.sec_limit' _item.category_id em_map _item.mandatory_code no _item_type.code float save_ save__em_map.plane_group _item_description.description ; Description of any plane group present ; _item.name '_em_map.plane_group' _item.category_id em_map _item.mandatory_code no _item_type.code text save_ save__em_map.origin_x _item_description.description ; The x origin of the map. ; _item.name '_em_map.origin_x' _item.category_id em_map _item.mandatory_code yes _item_type.code int save_ save__em_map.origin_y _item_description.description ; The y origin of the map. ; _item.name '_em_map.origin_y' _item.category_id em_map _item.mandatory_code yes _item_type.code int save_ save__em_map.origin_z _item_description.description ; The z origin of the map. ; _item.name '_em_map.origin_z' _item.category_id em_map _item.mandatory_code yes _item_type.code int save_ save__em_map.value_density_min _item_description.description ; Minimum density value in the map. ; _item.name '_em_map.value_density_min' _item.category_id em_map _item.mandatory_code yes _item_type.code float save_ save__em_map.value_density_max _item_description.description ; Maximum density value in the map. ; _item.name '_em_map.value_density_max' _item.category_id em_map _item.mandatory_code yes _item_type.code float save_ save__em_map.value_density_mean _item_description.description ; Mean (average) density value of the map. ; _item.name '_em_map.value_density_mean' _item.category_id em_map _item.mandatory_code yes _item_type.code float save_ save__em_map.details _item_description.description ; Any additional details about the map. ; _item.name '_em_map.details' _item.category_id em_map _item.mandatory_code no _item_type.code text save_ save__em_map.value_density_std _item_description.description ; The standard deviation density value of the map. ; _item.name '_em_map.value_density_std' _item.category_id em_map _item.mandatory_code yes _item_type.code float save_ save__em_map.id _item_description.description ; Unique identifier of the volume map. ; _item.name '_em_map.id' _item.category_id em_map _item.mandatory_code yes _item_type.code code save_ save__em_map.2d_crystal_grow_id _item_description.description ; This data item is a pointer to the 2D_CRYSTAL_GROW category. ; _item.name '_em_map.2d_crystal_grow_id' _item.category_id em_map _item.mandatory_code no _item_type.code code # _item_linked.child_name '_em_map.2d_crystal_grow_id' # _item_linked.parent_name '_em_2d_crystal_grow.id' save_ save__em_map.map_symmetry_id _item_description.description ; This data item is a pointer to the EM_SYMMETRY category. ; _item.name '_em_map.map_symmetry_id' _item.category_id em_map _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_map.map_symmetry_id' _item_linked.parent_name '_em_map_symmetry.id' save_ save__em_map.map_structure_factors_id _item_description.description ; This data item is a pointer to the MAP_STRUCTURE_FACTORS category. ; _item.name '_em_map.map_structure_factors_id' _item.category_id em_map _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_map.map_structure_factors_id' _item_linked.parent_name '_em_map_structure_factors.id' save_ save__em_map.cell_length_a _item_description.description ; Unit cell length a. ; _item.name '_em_map.cell_length_a' _item.category_id em_map _item.mandatory_code yes _item_type.code float save_ save__em_map.cell_length_b _item_description.description ; Unit cell length b. ; _item.name '_em_map.cell_length_b' _item.category_id em_map _item.mandatory_code yes _item_type.code float save_ save__em_map.cell_length_c _item_description.description ; Unit cell length c. ; _item.name '_em_map.cell_length_c' _item.category_id em_map _item.mandatory_code yes _item_type.code float save_ save__em_map.cell_length_a_esd _item_description.description ; Error standard deviation of unit cell length a. ; _item.name '_em_map.cell_length_a_esd' _item.category_id em_map _item.mandatory_code yes _item_type.code float save_ save__em_map.cell_length_b_esd _item_description.description ; Error standard deviation of unit cell length b. ; _item.name '_em_map.cell_length_b_esd' _item.category_id em_map _item.mandatory_code yes _item_type.code float save_ save__em_map.cell_length_c_esd _item_description.description ; Error standard deviation of unit cell length c. ; _item.name '_em_map.cell_length_c_esd' _item.category_id em_map _item.mandatory_code yes _item_type.code float save_ save__em_map.cell_angle_alpha _item_description.description ; Value of unit cell angle alpha in degrees. ; _item.name '_em_map.cell_angle_alpha' _item.category_id em_map _item.mandatory_code yes _item_type.code float save_ save__em_map.cell_angle_beta _item_description.description ; Value of unit cell angle beta in degrees. ; _item.name '_em_map.cell_angle_beta' _item.category_id em_map _item.mandatory_code yes _item_type.code float save_ save__em_map.cell_angle_gamma _item_description.description ; Value of unit cell angle gamma in degrees. ; _item.name '_em_map.cell_angle_gamma' _item.category_id em_map _item.mandatory_code yes _item_type.code float save_ save__em_map.reflection_wavelength _item_description.description ; Wavelength of electrons in angstroms. ; _item.name '_em_map.reflection_wavelength' _item.category_id em_map _item.mandatory_code no _item_type.code float save_ save__em_map.r_value_all_data _item_description.description ; The R-factor value compares overall agreement between the amplitudes of two sets of structure factors as follows: R= sigma || Fobs | - | Fcalc || / sigma | Fobs | For each reflection the magnitude of the computed difference between the observed structure-factor amplitude from the native data set |Fobs| and the calculated amplitude from the model in its current trial location |Fcalc| is summed for all reflections and divided by the sum of the observed structure factors. ; _item.name '_em_map.r_value_all_data' _item.category_id em_map _item.mandatory_code no _item_type.code float save_ save__em_map.r_free _item_description.description ; The R-free statistic value measures the agreement between the atomic model and the diffraction data for a 'test' set of reflections (usually 10%) that is omitted during refinement. ; _item.name '_em_map.r_free' _item.category_id em_map _item.mandatory_code no _item_type.code float save_ save__em_map.num_atoms _item_description.description ; The number of atoms. ; _item.name '_em_map.num_atoms' _item.category_id em_map _item.mandatory_code yes _item_type.code int save_ save__em_map.num_observations _item_description.description ; The number of observations. ; _item.name '_em_map.num_observations' _item.category_id em_map _item.mandatory_code no _item_type.code int save_ save__em_map.num_unique_reflns _item_description.description ; The number of unique electron reflections collected. ; _item.name '_em_map.num_unique_reflns' _item.category_id em_map _item.mandatory_code no _item_type.code int save_ save__em_map.percent_reflns_collected _item_description.description ; The percentage of possible reflections collected to specified resolution. ; _item.name '_em_map.percent_reflns_collected' _item.category_id em_map _item.mandatory_code no _item_type.code line save_ save__em_map.map_eigenvalues_id _item_description.description ; Pointer to the MAP_EIGENVALUES category. ; _item.name '_em_map.map_eigenvalues_id' _item.category_id em_map _item.mandatory_code no _item_type.code code save_ save__em_map.handedness_method _item_description.description ; The method used to determine the hand of the virus. The hand is fixed for the reconstruction by combining the projections in a consistent way. Information gleaned from pairs of images of tilted particles must be used to validate a particular choice of hand. ; _item.name '_em_map.handedness_method' _item.category_id em_map _item.mandatory_code no _item_type.code text save_ save__em_map.phase_origin_method _item_description.description ; The method used to determine the phase origin of the virus map. ; _item.name '_em_map.phase_origin_method' _item.category_id em_map _item.mandatory_code no _item_type.code text save_ save__em_map.num_class_averages _item_description.description ; The number of class averages (one class average contains images that are the same) resulting from the multivariate statistical analysis of the individual images of particles are 2d projections of a 3d structure in different projection directions. Given a sufficiently large number of good 2d projections the 3d structure can be reconstructed knowing the orientational relationship between all the projection class averages. For an entirely asymmetric particle at least three different projections are required to solve the orientation problem. ; _item.name '_em_map.num_class_averages' _item.category_id em_map _item.mandatory_code no _item_type.code text save_ save__em_map.axisOrderFast _item_description.description ; The map axis order fast ; _item.name '_em_map.axisOrderFast' _item.category_id em_map _item.mandatory_code no _item_type.code line save_ save__em_map.axisOrderMedium _item_description.description ; The map axis order fast ; _item.name '_em_map.axisOrderMedium' _item.category_id em_map _item.mandatory_code no _item_type.code line save_ save__em_map.axisOrderSlow _item_description.description ; The map axis order slow ; _item.name '_em_map.axisOrderSlow' _item.category_id em_map _item.mandatory_code no _item_type.code line save_ save__em_map.spaceGroupNumber _item_description.description ; The space group number for the map ; _item.name '_em_map.spaceGroupNumber' _item.category_id em_map _item.mandatory_code no _item_type.code line save_ save__em_map.isosurface_countour_level _item_description.description ; The isosurface_countour_level for the map ; _item.name '_em_map.isosurface_countour_level' _item.category_id em_map _item.mandatory_code no _item_type.code float save_ save__em_map.author_threshold _item_description.description ; The author_threshold for isosurface_countour_level for the map ; _item.name '_em_map.author_threshold' _item.category_id em_map _item.mandatory_code yes _item_type.code float save_ save__em_map.contrast_convention _item_description.description ; The contrast convention used for the map ; _item.name '_em_map.contrast_convention' _item.category_id em_map _item.mandatory_code yes _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail P 'protein positive' N 'protein negative' save_ save__em_map.enforced_symmetry _item_description.description ; Description of any enforced symmetry present in the map ; _item.name '_em_map.enforced_symmetry' _item.category_id em_map _item.mandatory_code no _item_type.code text save_ save__em_map.local_symmetry_details _item_description.description ; Description of any local symmetry present in the map ; _item.name '_em_map.local_symmetry_details' _item.category_id em_map _item.mandatory_code no _item_type.code text save_ save__em_map.thickness _item_description.description ; for 2d crystals the thickness ; _item.name '_em_map.thickness' _item.category_id em_map _item.mandatory_code no _item_type.code float save_ save__em_map.release_date _item_description.description ; Date (YYYY-MM-DD) of map release ; _item.name '_em_map.release_date' _item.category_id em_map _item.mandatory_code yes _item_type.code yyyy-mm-dd _item_examples.case '2001-05-08' save_ ########################### ## EM_MAP_CTF_CORRECTION ## ########################### save_em_map_ctf_correction _category.description ; Data items in the EM_MAP_CTF_CORRECTION category record details about the CTF correction method. ; _category.id em_map_ctf_correction _category.mandatory_code no loop_ _category_key.name '_em_map_ctf_correction.id' '_em_map_ctf_correction.map_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_map_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_map_ctf_correction.id 1 _em_map_ctf_correction.map_id 1 _em_map_ctf_correction.method . _em_map_ctf_correction.details . ; save_ save__em_map_ctf_correction.id _item_description.description ; Unique identifier for CTF correction of the map. ; _item.name '_em_map_ctf_correction.id' _item.category_id em_map_ctf_correction _item.mandatory_code yes _item_type.code code save_ save__em_map_ctf_correction.map_id _item_description.description ; This data item is a pointer to the EM_MAP category. ; _item.name '_em_map_ctf_correction.map_id' _item.category_id em_map_ctf_correction _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_map_ctf_correction.map_id' _item_linked.parent_name '_em_map.id' save_ save__em_map_ctf_correction.method _item_description.description ; The method used to correct for the image distortions introduced by the phase contrast transfer function (CTF). CTF correction could be applied to the entire scanned micrograph or alternatively they may be applied to the extracted images of individual particles or at the end of the analysis to the density map reconstructed from the micrograph. ; _item.name '_em_map_ctf_correction.method' _item.category_id em_map_ctf_correction _item.mandatory_code no _item_type.code text save_ save__em_map_ctf_correction.details _item_description.description ; Any additional details about ctf correction. ; _item.name '_em_map_ctf_correction.details' _item.category_id em_map_ctf_correction _item.mandatory_code no _item_type.code line save_ ############################## ## EM_MAP_STRUCTURE FACTORS ## ############################## save_em_map_structure_factors _category.description ; Data items in the EM_MAP_STRUCTURE_FACTORS category record details about structure factors relating to the map. These are uploaded in a file. ; _category.id em_map_structure_factors _category.mandatory_code no loop_ _category_key.name '_em_map_structure_factors.id' '_em_map_structure_factors.map_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_map_group' loop_ _category_examples.detail _category_examples.case ;Example 1 - ; ; _em_map_structure_factors.id 1 _em_map_structure_factors.map_id 1 _em_map_structure_factors.method . _em_map_structure_factors.details . _em_map_structure_factors.map_file_id file1 ; save_ save__em_map_structure_factors.id _item_description.description ; Unique identifier of the map structure factors. ; _item.name '_em_map_structure_factors.id' _item.category_id em_map_structure_factors _item.mandatory_code yes _item_type.code code save_ save__em_map_structure_factors.map_id _item_description.description ; This data item is a pointer to the MAP category. ; _item.name '_em_map_structure_factors.map_id' _item.category_id em_map_structure_factors _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_map_structure_factors.map_id' _item_linked.parent_name '_em_map.id' save_ save__em_map_structure_factors.method _item_description.description ; A description of how the structure factors of the masked cryo-EM maps were calculated. For example structure factors could be calculated by Fourier transformation using the progrma SFALL of the CCP4 package. ; _item.name '_em_map_structure_factors.method' _item.category_id em_map_structure_factors _item.mandatory_code no _item_type.code text save_ save__em_map_structure_factors.details _item_description.description ; Any additional details about the structure factors file. ; _item.name '_em_map_structure_factors.details' _item.category_id em_map_structure_factors _item.mandatory_code no _item_type.code text save_ save__em_map_structure_factors.map_files_id _item_description.description ; Pointer to the MAP_FILES category. ; _item.name '_em_map_structure_factors.map_files_id' _item.category_id em_map_structure_factors _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_map_structure_factors.map_files_id' _item_linked.parent_name '_em_map_files.id' save_ ###################### ### EM_MAP_SYMMETRY ## ###################### save_em_map_symmetry _category.description ; Data items in the EM_MAP_SYMMETRY category record details about the symmetry of the assembly in the map. ; _category.id em_map_symmetry _category.mandatory_code yes _category_key.name '_em_map_symmetry.map_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_map_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_map_symmetry.map_id 1 _em_map_symmetry.id 1 _em_map_symmetry.plane_group_name_H-M . _em_map_symmetry.enforced_symmetry . _em_map_symmetry.equiv_pos_as_xyz . ; save_ save__em_map_symmetry.id _item_description.description ; Unique identifier of the map symmetry. ; _item.name '_em_map_symmetry.id' _item.category_id em_map_symmetry _item.mandatory_code yes _item_type.code code save_ save__em_map_symmetry.map_id _item_description.description ; This data item is a pointer the MAP category. ; _item.name '_em_map_symmetry.map_id' _item.category_id em_map_symmetry _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_map_symmetry.map_id' _item_linked.parent_name '_em_map.id' save_ save__em_map_symmetry.plane_group_name_H-M _item_description.description ; This is the plane group described using Herman Maugin nomenclature. ; _item.name '_em_map_symmetry.plane_group_name_H-M' _item.category_id em_map_symmetry _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value P1 P2 P12 P121 C12 P222 P221 P22121 C222 P4 P422 P4212 P3 P321 P312 P6 P622 save_ save__em_map_symmetry.enforced_symmetry _item_description.description ; This is the enforced symmetry applied to the map. ; _item.name '_em_map_symmetry.enforced_symmetry' _item.category_id em_map_symmetry _item.mandatory_code no _item_type.code line save_ save__em_map_symmetry.equiv_pos_as_xyz _item_description.description ; This is an equivalent xyz position. ; _item.name '_em_map_symmetry.equiv_pos_as_xyz' _item.category_id em_map_symmetry _item.mandatory_code no _item_type.code line save_ ################################# ### EM_MAP_ORTHOGONAL_SLICES ## ################################# save_em_orthogonal_slices _category.description ; Data items in the EM_ORTHOGONAL_SLICES category record details about orthogonal slices through the map. These consist of an x-slice, y-slice and z-slice through the map. ; _category.id em_orthogonal_slices _category.mandatory_code yes loop_ _category_key.name '_em_orthogonal_slices.map_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ;Example 1 - ; ; _em_orthogonal_slices.id 1 _em_orthogonal_slices.map_id 1 _em_orthogonal_slices.x_slice_id 1 _em_orthogonal_slices.y_slice_id 1 _em_orthogonal_slices.z_slice_id 1 _em_orthogonal_slices.x_slice_number 1 _em_orthogonal_slices.y_slice_number 1 _em_orthogonal_slices.z_slice_number 1 ; save_ save__em_orthogonal_slices.id _item_description.description ; This data item is a unique identifier for the ORTHOGONAL_SLICES category. ; _item.name '_em_orthogonal_slices.id' _item.category_id em_orthogonal_slices _item.mandatory_code yes _item_type.code code save_ save__em_orthogonal_slices.map_id _item_description.description ; This data item is a pointer to the MAP category. ; _item.name '_em_orthogonal_slices.map_id' _item.category_id em_orthogonal_slices _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_orthogonal_slices.map_id' _item_linked.parent_name '_em_map.id' save_ save__em_orthogonal_slices.x_slice_id _item_description.description ; The orthogonal x slice id. ; _item.name '_em_orthogonal_slices.x_slice_id' _item.category_id em_orthogonal_slices _item.mandatory_code yes _item_type.code line save_ save__em_orthogonal_slices.y_slice_id _item_description.description ; The orthogonal y slice id. ; _item.name '_em_orthogonal_slices.y_slice_id' _item.category_id em_orthogonal_slices _item.mandatory_code yes _item_type.code line save_ save__em_orthogonal_slices.z_slice_id _item_description.description ; The orthogonal z slice id. ; _item.name '_em_orthogonal_slices.z_slice_id' _item.category_id em_orthogonal_slices _item.mandatory_code yes _item_type.code line save_ save__em_orthogonal_slices.x_slice_number _item_description.description ; The orthogonal x slice number. ; _item.name '_em_orthogonal_slices.x_slice_number' _item.category_id em_orthogonal_slices _item.mandatory_code no _item_type.code line save_ save__em_orthogonal_slices.y_slice_number _item_description.description ; The orthogonal y slice number. ; _item.name '_em_orthogonal_slices.y_slice_number' _item.category_id em_orthogonal_slices _item.mandatory_code no _item_type.code line save_ save__em_orthogonal_slices.z_slice_number _item_description.description ; The orthogonal z slice number. ; _item.name '_em_orthogonal_slices.z_slice_number' _item.category_id em_orthogonal_slices _item.mandatory_code no _item_type.code line save_ #################### ### EM_MAP_FIGURE ## #################### save_em_map_figure _category.description ; Data items in the EM_MAP_FIGURE record details about figures associated with the map. These can consist of figures with associated text which are related to the map. ; _category.id em_map_figure _category.mandatory_code no loop_ _category_key.name '_em_map_figure.id' '_em_map_figure.map_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_map_group' loop_ _category_examples.detail _category_examples.case ;Example 1 - ; ; _em_map_figure.id 1 _em_map_figure.map_id 1 _em_map_figure.num_bytes 1000 _em_map_figure.details . _em_map_figure.map_files_id file1 ; save_ save__em_map_figure.id _item_description.description ; Unique identifier of the figure assembly. ; _item.name '_em_map_figure.id' _item.category_id em_map_figure _item.mandatory_code yes _item_type.code code save_ save__em_map_figure.map_id _item_description.description ; This data item is a pointer to the EM_MAP category. ; _item.name '_em_map_figure.map_id' _item.category_id em_map_figure _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_map_figure.map_id' _item_linked.parent_name '_em_map.id' save_ save__em_map_figure.num_bytes _item_description.description ; The number of bytes in the image file. ; _item.name '_em_map_figure.num_bytes' _item.category_id em_map_figure _item.mandatory_code no _item_type.code float save_ save__em_map_figure.details _item_description.description ; Any additional details about the figure uploaded with the map. These could include captions. ; _item.name '_em_map_figure.details' _item.category_id em_map_figure _item.mandatory_code no _item_type.code text save_ save__em_map_figure.map_files_id _item_description.description ; Unique identifier of the figure assembly. ; _item.name '_em_map_figure.map_files_id' _item.category_id em_map_figure _item.mandatory_code yes _item_type.code code save_ ############################### ### EM_MAP_SURFACE_RENDERING ## ############################### # save_em_map_surface_rendering _category.description ; Data items in the EM_MAP_SURFACE_RENDERING category record details about surface rendering of the map. The surface of the map has to be defined and 'rendered' to make understandable images. The quality of the structure can be judged visually by looking at the high-resolution texture of the molecular surface. It can make sense to threshold/interpret data to 100% (or up to 120%) of the expected volume of the molecular assembly which has been calculated from the molecular mass. To emphasize the fine structures in the map thresholding values as little as 25% may be used. ; _category.id em_map_surface_rendering _category.mandatory_code yes loop_ _category_key.name '_em_map_surface_rendering.id' '_em_map_surface_rendering.map_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_map_group' loop_ _category_examples.detail _category_examples.case ;Example 1 - ; ; _em_map_surface_rendering.id 1 _em_map_surface_rendering.map_id 1 _em_map_surface_rendering.method . _em_map_surface_rendering.threshold_volume_mol_wt . _em_map_surface_rendering.details . _em_map_surface_rendering.map_files_id file1 ; save_ save__em_map_surface_rendering.id _item_description.description ; Unique identifier of the surface rendered image figure of the assembly. ; _item.name '_em_map_surface_rendering.id' _item.category_id em_map_surface_rendering _item.mandatory_code yes _item_type.code code save_ save__em_map_surface_rendering.map_id _item_description.description ; This data item is a pointer to the EM_MAP category. ; _item.name '_em_map_surface_rendering.map_id' _item.category_id em_map_surface_rendering _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_map_surface_rendering.map_id' _item_linked.parent_name '_em_map.id' save_ save__em_map_surface_rendering.method _item_description.description ; The method used to obtain the surface rendered image. ; _item.name '_em_map_surface_rendering.method' _item.category_id em_map_surface_rendering _item.mandatory_code no _item_type.code text save_ save__em_map_surface_rendering.threshold_volume_mol_wt _item_description.description ; The threshold volume molecular weight (as a percentage) used to produce the surface rendered image. ; _item.name '_em_map_surface_rendering.threshold_volume_mol_wt' _item.category_id em_map_surface_rendering _item.mandatory_code no _item_type.code float save_ save__em_map_surface_rendering.details _item_description.description ; Any additional details about the surface rendered image. ; _item.name '_em_map_surface_rendering.details' _item.category_id em_map_surface_rendering _item.mandatory_code no _item_type.code float save_ save__em_map_surface_rendering.map_files_id _item_description.description ; This data item is a pointer to the EM_FILES category. ; _item.name '_em_map_surface_rendering.map_files_id' _item.category_id em_map_surface_rendering _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_map_surface_rendering.map_files_id' _item_linked.parent_name '_em_map_files.id' save_ ################### ### EM_MAP_FILES ## ################### save_em_map_files _category.description ; Data items in the EM_MAP_FILES category record details about files relating to the map. These files can be uploaded and include files containing information about ; _category.id em_map_files _category.mandatory_code no loop_ _category_key.name '_em_map_files.id' '_em_map_files.map_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_map_group' loop_ _category_examples.detail _category_examples.case ;Example 1 - ; ; _em_map_files.id 1 _em_map_files.map_id 1 _em_map_files.details . ; save_ save__em_map_files.id _item_description.description ; Unique identifier of the MAP_FILES category. ; _item.name '_em_map_files.id' _item.category_id em_map_files _item.mandatory_code yes _item_type.code code save_ save__em_map_files.map_id _item_description.description ; This data item is a pointer to the EM_MAP category. ; _item.name '_em_map_files.map_id' _item.category_id em_map_files _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_map_files.map_id' _item_linked.parent_name '_em_map.id' save_ save__em_map_files.orthogonal_slices_x_slice_id _item_description.description ; The orthogonal slices x_slice file identifier. ; _item.name '_em_map_files.orthogonal_slices_x_slice_id' _item.category_id em_map_files _item.mandatory_code no _item_type.code code save_ save__em_map_files.orthogonal_slices_y_slice_id _item_description.description ; The orthogonal slices y_slice file identifier. ; _item.name '_em_map_files.orthogonal_slices_y_slice_id' _item.category_id em_map_files _item.mandatory_code no _item_type.code code save_ save__em_map_files.orthogonal_slices_z_slice_id _item_description.description ; The orthogonal slices z_slice file identifier. ; _item.name '_em_map_files.orthogonal_slices_z_slice_id' _item.category_id em_map_files _item.mandatory_code no _item_type.code code save_ save__em_map_files.details _item_description.description ; Any additional details about the files. ; _item.name '_em_map_files.details' _item.category_id em_map_files _item.mandatory_code no _item_type.code text save_ ######################### ### EM_MAP_EIGENVALUES ## ######################### save_em_map_eigenvalues _category.description ; Data items in the EM_MAP_EIGENVALUES category record details about values of the eigenvectors for projection sets. 2d projection images are considered as a linear combination of the main eigenvectors 'eigenimages' of the projection set, enabling a reduction of the total amount of data and simplifying its interpretation. The eigenvalue spectrum gives an indication of the randomness of the data that is included in the reconstruction. The completeness of the data can be verified eg all eigenvalues exceeded 1.0. ; _category.id em_map_eigenvalues _category.mandatory_code yes loop_ _category_key.name '_em_map_eigenvalues.id' '_em_map_eigenvalues.map_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_map_group' loop_ _category_examples.detail _category_examples.case ;Example 1 - ; ; _em_map_eigenvalues.id 1 _em_map_eigenvalues.map_id 1 _em_map_eigenvalues.number_eigenimages . _em_map_eigenvalues.details . _em_map_eigenvalues.spectrum . _em_map_eigenvalues.min_value . _em_map_eigenvalues.max_value . ; save_ save__em_map_eigenvalues.id _item_description.description ; Unique identifier of the EIGENVALUES category. ; _item.name '_em_map_eigenvalues.id' _item.category_id em_map_eigenvalues _item.mandatory_code yes _item_type.code code save_ save__em_map_eigenvalues.map_id _item_description.description ; This data item is a pointer to the EM_MAP category. ; _item.name '_em_map_eigenvalues.map_id' _item.category_id em_map_eigenvalues _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_map_eigenvalues.map_id' _item_linked.parent_name '_em_map.id' save_ save__em_map_eigenvalues.details _item_description.description ; Any additional details about the eigenvalues. ; _item.name '_em_map_eigenvalues.details' _item.category_id em_map_eigenvalues _item.mandatory_code no _item_type.code text save_ save__em_map_eigenvalues.spectrum _item_description.description ; A description of the eigenvalue spectrum for the data set used in the 3d reconstruction for the map. A data set consisting of pure noise has a characteristic eigenvalue spectrum which depends on the number of images, the number of image elements and the noise statistics. Since the eigenvalues are only determined by the spacing and number of the sample points, the eigenvalue spectrum is not affected by the signal to noise in the data or the reliability of the orientations. This information is seen from the resolution dependence of the phase residual seen during refinement. For the eigenvectors to be significant, the associated eigenvalues should stand out from the noise eigenvalue spectrum. ; _item.name '_em_map_eigenvalues.spectrum' _item.category_id em_map_eigenvalues _item.mandatory_code no _item_type.code text save_ save__em_map_eigenvalues.min_value _item_description.description ; The minimum eigenvalue. A low inverse eigenvalue indicates that many, well-spaced samples have been averaged to generate the coefficient while a high one indicates that only a few sample points were used so that the coefficient is more susceptible to noise. ; _item.name '_em_map_eigenvalues.min_value' _item.category_id em_map_eigenvalues _item.mandatory_code no _item_type.code float save_ save__em_map_eigenvalues.max_value _item_description.description ; The maximum eigenvalue. A low inverse eigenvalue indicates that many, well-spaced samples have been averaged to generate the coefficient while a high one indicates that only a few sample points were used so that the coefficient is more susceptible to noise. ; _item.name '_em_map_eigenvalues.max_value' _item.category_id em_map_eigenvalues _item.mandatory_code no _item_type.code float save_ ##################### ### EM_TOMOGRAPHY ## ##################### save_em_tomography _category.description ; Electron tomography allows the structural organisation of individual cells and organelles and bacterial cells to be studied at nanometre resolution. The samples are unique objects which precludes averaging over many copies so that tomograms are built from images of a tilt series taken from a single copy of the object. ; _category.id em_tomography _category.mandatory_code no _category_key.name '_em_tomography.id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_tomography_group' save_ save__em_tomography.id _item_description.description ; The value of _em_tomography.id must uniquely identify a collection of observed complexes. ; _item.name '_em_tomography.id' _item.category_id em_tomography _item.mandatory_code yes _item_type.code code save_ save__em_tomography.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_tomography.entry_id' _item.category_id em_tomography _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_tomography.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_tomography.tilt_angle_incr _item_description.description ; Tilt angle increment in (degrees) used in reconstruction of tomographic map. ; _item.name '_em_tomography.tilt_angle_incr' _item.category_id em_tomography _item.mandatory_code no _item_type.code float save_ save__em_tomography.num_sections _item_description.description ; Number of sections used in reconstruction of tomographic map. ; _item.name '_em_tomography.num_sections' _item.category_id em_tomography _item.mandatory_code no _item_type.code int save_ save__em_tomography.details _item_description.description ; General details on the tomographic experiment ; _item.name '_em_tomography.details' _item.category_id em_tomography _item.mandatory_code no _item_type.code text save_ save__em_tomography.StagePositionX _item_description.description ; the StagePosition in X ; _item.name '_em_tomography.StagePositionX' _item.category_id em_tomography _item.mandatory_code no _item_type.code float save_ save__em_tomography.StagePositionY _item_description.description ; the StagePosition in Y ; _item.name '_em_tomography.StagePositionY' _item.category_id em_tomography _item.mandatory_code no _item_type.code float save_ ########################### ### EM_TOMOGRAPHY_IMAGE ## ########################### save_em_tomography_image _category.description ; Data items in the EM_TOMOGRAPHY_IMAGE category record details of each of the images collected ; _category.id em_tomography_image _category.mandatory_code no _category_key.name '_em_tomography_image.id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_tomography_group' save_ save__em_tomography_image.id _item_description.description ; The value of _em_tomography_image.id must uniquely identify each tilted image ; _item.name '_em_tomography_image.id' _item.category_id em_tomography_image _item.mandatory_code yes _item_type.code code save_ save__em_tomography_image.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_tomography_image.entry_id' _item.category_id em_tomography_image _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_tomography.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_tomography_image.defocus _item_description.description ; The defocus used for each image ; _item.name '_em_tomography_image.defocus' _item.category_id em_tomography_image _item.mandatory_code yes _item_type.code float save_ save__em_tomography_image.electron_dose _item_description.description ; The electron_dose used for each image ; _item.name '_em_tomography_image.electron_dose' _item.category_id em_tomography_image _item.mandatory_code yes _item_type.code float save_ save__em_tomography_image.exposure_time _item_description.description ; The exposure_time used for each image ; _item.name '_em_tomography_image.exposure_time' _item.category_id em_tomography_image _item.mandatory_code yes _item_type.code float save_ save__em_tomography_image.magnification _item_description.description ; The magnification used for each image ; _item.name '_em_tomography_image.magnification' _item.category_id em_tomography_image _item.mandatory_code yes _item_type.code float save_ save__em_tomography_image.pixel_size _item_description.description ; The pixel_size used for each image ; _item.name '_em_tomography_image.pixel_size' _item.category_id em_tomography_image _item.mandatory_code yes _item_type.code float save_ save__em_tomography_image.shift_x _item_description.description ; The shift in x used for each image ; _item.name '_em_tomography_image.shift_x' _item.category_id em_tomography_image _item.mandatory_code yes _item_type.code float save_ save__em_tomography_image.shift_y _item_description.description ; The shift in y used for each image ; _item.name '_em_tomography_image.shift_y' _item.category_id em_tomography_image _item.mandatory_code yes _item_type.code float save_ save__em_tomography_image.tilt_angle _item_description.description ; The tilt_angle used for each image ; _item.name '_em_tomography_image.tilt_angle' _item.category_id em_tomography_image _item.mandatory_code yes _item_type.code float save_ ############################# ## EM_ELECTRON_DIFFRACTION ## ############################# save_em_electron_diffraction _category.description ; The EM_ELECTRON_DIFFRACTION category records basic information about electron diffraction experiment. ; _category.id em_electron_diffraction _category.mandatory_code no loop_ _category_key.name '_em_electron_diffraction.id' '_em_electron_diffraction.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_data_collection_group' 'em_2D_crystal_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1TUB and laboratory records for the structure corresponding to PDB entry 1TUB ; ; _em_electron_diffraction.entry_id 1TUB _em_electron_diffraction.id 1 _em_electron_diffraction.num_unique_reflections 12000 _em_electron_diffraction.num_diff_patterns 94 _em_electron_diffraction.num_images 149 _em_electron_diffraction.tilt_range_min 0 _em_electron_diffraction.tilt_range_max 55 _em_electron_diffraction.d_res_high 3.7 _em_electron_diffraction.details . ; save_ save__em_electron_diffraction.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_electron_diffraction.entry_id' _item.category_id em_electron_diffraction _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_electron_diffraction.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_electron_diffraction.id _item_description.description ; The value of _electron_diffraction.id must uniquely identify the electron diffraction experiment. ; _item.name '_em_electron_diffraction.id' _item.category_id em_electron_diffraction _item.mandatory_code yes _item_type.code code save_ save__em_electron_diffraction.num_diff_patterns _item_description.description ; The number of diffraction patterns collected in the electron diffraction experiment. ; _item.name '_em_electron_diffraction.num_diff_patterns' _item.category_id em_electron_diffraction _item.mandatory_code no _item_type.code int save_ save__em_electron_diffraction.num_images _item_description.description ; The number of 2D crystal images collected in the electron diffraction experiment. ; _item.name '_em_electron_diffraction.num_images' _item.category_id em_electron_diffraction _item.mandatory_code no _item_type.code int save_ save__em_electron_diffraction.tilt_range_min _item_description.description ; The minimum tilt angle used in the electron diffraction experiment. ; _item.name '_em_electron_diffraction.tilt_range_min' _item.category_id em_electron_diffraction _item.mandatory_code no _item_type.code float save_ save__em_electron_diffraction.tilt_range_max _item_description.description ; The maximum tilt angle used in the electron diffraction experiment. ; _item.name '_em_electron_diffraction.tilt_range_max' _item.category_id em_electron_diffraction _item.mandatory_code no _item_type.code float save_ save__em_electron_diffraction.num_unique_reflections _item_description.description ; The number of unique structure factors from the electron diffraction experiment. ; _item.name '_em_electron_diffraction.num_unique_reflections' _item.category_id em_electron_diffraction _item.mandatory_code no _item_type.code int _item_examples.case '12000' save_ save__em_electron_diffraction.num_reflections_total _item_description.description ; The total number of structure factors measured in the electron diffraction experiment, before merging to a unique set. ; _item.name '_em_electron_diffraction.num_reflections_total' _item.category_id em_electron_diffraction _item.mandatory_code no _item_type.code int _item_examples.case '25743' save_ save__em_electron_diffraction.d_res_high _item_description.description ; the highest resolution d-value for the electron diffraction experiment. ; _item.name '_em_electron_diffraction.d_res_high' _item.category_id em_electron_diffraction _item.mandatory_code no _item_type.code int _item_examples.case '5.0' save_ save__em_electron_diffraction.overall_error _item_description.description ; the overall phase error in degrees. ; _item.name '_em_electron_diffraction.overall_error' _item.category_id em_electron_diffraction _item.mandatory_code no _item_type.code int save_ save__em_electron_diffraction.rejection_criteria_error _item_description.description ; the rejection criteria (phase error) in degrees. ; _item.name '_em_electron_diffraction.rejection_criteria_error' _item.category_id em_electron_diffraction _item.mandatory_code no _item_type.code int save_ save__em_electron_diffraction.details _item_description.description ; Details of the electron diffraction experiment ; _item.name '_em_electron_diffraction.details' _item.category_id em_electron_diffraction _item.mandatory_code yes _item_type.code text loop_ _item_examples.case _item_examples.detail 1 ; THE MODEL WAS DERIVED USING ELECTRON DIFFRACTION AND IMAGE DATA FROM TWO DIMENSIONAL CRYSTALS OF TUBULIN INDUCED BY THE PRESENCE OF ZN++ IONS. WHAT FOLLOWS ARE THE COORDINATES FOR THE AB-TUBULIN DIMER BOUND TO TAXOL AS OBTAINED BY ELECTRON CRYSTALLOGRAPHY OF ZINC-INDUCED SHEETS. THIS IS THE UNREFINED MODEL, BUILT INTO A RAW DENSITY MAP WHERE THE RESOLUTION IN THE PLANE OF THE SHEET WAS 3.7 ANGSTROMS AND THAT PERPENDICULAR TO THE SHEET ABOUT 4.8 ANGSTROMS. THE MODEL DOES NOT CONTAIN MOST OF THE C-TERMINAL RESIDUES OF EITHER MONOMER WHICH WERE DISORDERED IN THE MAP. THE LOOP BETWEEN HELIX H1 AND STRAND S2, AND THAT BETWEEN H2 AND S3 ARE PRESENT FOR COMPLETENESS BUT WERE BUILT INTO VERY WEAK DENSITY. GIVEN THE LIMITED RESOLUTION OF THE MAP, THE CONFORMATION OF THE SIDE CHAINS, ESPECIALLY THOSE CORRESPONDING TO RESIDUES ON THE SURFACE OF THE DIMER, MUST BE TAKEN CAUTIOUSLY. IN ADDITION, BECAUSE THIS IS AN UNREFINED MODEL, CERTAIN GEOMETRY ERRORS MAY STILL BE PRESENT IN THE STRUCTURE. PLEASE TAKE THIS INTO ACCOUNT WHEN INTERPRETING YOUR OWN DATA BASED ON THE PRESENT TUBULIN STRUCTURE. ALTHOUGH THE POSITION OF RESIDUES (WITH THE EXCEPTION OF THOSE IN THE LOOPS MENTIONED ABOVE) SHOULD NOT CHANGE SIGNIFICANTLY UPON REFINEMENT, DRAWING INFORMATION AT THE LEVEL OF SIDE CHAIN CONFORMATION IS CLEARLY NOT ADVISED. FINALLY, PLEASE NOTICE THAT THE TAXOID IN THE MODEL IS THE TAXOL DERIVATIVE TAXOTERE. ; save_ ######################################## ## EM_ELECTRON_DIFFRACTION_TILT_ANGLE ## ######################################## save_em_electron_diffraction_tilt_angle _category.description ; data items in the em_electron_diffraction_tilt_angle category record details about data collected at a specific tilt angle. ; _category.id em_electron_diffraction_tilt_angle _category.mandatory_code no loop_ _category_key.name '_em_electron_diffraction_tilt_angle.id' '_em_electron_diffraction_tilt_angle.electron_diffraction_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_data_collection_group' 'em_2D_crystal_group' loop_ _category_examples.detail _category_examples.case ;based on pdb entry 1TUB ; ; loop_ _em_electron_diffraction_tilt_angle.electron_diffraction_id _em_electron_diffraction_tilt_angle.id _em_electron_diffraction_tilt_angle.tilt_angle _em_electron_diffraction_tilt_angle.num_patterns _em_electron_diffraction_tilt_angle.num_images 1 1 0 18 12 1 2 45 57 51 1 3 55 19 86 ; save_ save__em_electron_diffraction_tilt_angle.electron_diffraction_id _item_description.description ; this data item is a pointer to _em_electron_diffraction.id in the EM_ELECTRON_DIFFRACTION category. ; _item.name '_em_electron_diffraction_tilt_angle.electron_diffraction_id' _item.category_id em_electron_diffraction_tilt_angle _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_electron_diffraction_tilt_angle.electron_diffraction_id' _item_linked.parent_name '_em_electron_diffraction.id' save_ save__em_electron_diffraction_tilt_angle.id _item_description.description ; the value of _electron_diffraction_tilt_angle.id must uniquely identify the tilt angle. ; _item.name '_em_electron_diffraction_tilt_angle.id' _item.category_id em_electron_diffraction_tilt_angle _item.mandatory_code yes _item_type.code code save_ save__em_electron_diffraction_tilt_angle.tilt_angle _item_description.description ; the tilt angle at which diffraction data and/or images were obtained. ; _item.name '_em_electron_diffraction_tilt_angle.tilt_angle' _item.category_id em_electron_diffraction_tilt_angle _item.mandatory_code no _item_type.code float _item_examples.case '45.0' save_ save__em_electron_diffraction_tilt_angle.num_patterns _item_description.description ; the number of diffraction patterns measured at the specified tilt angle. ; _item.name '_em_electron_diffraction_tilt_angle.num_patterns' _item.category_id em_electron_diffraction_tilt_angle _item.mandatory_code no _item_type.code int _item_examples.case '57' save_ save__em_electron_diffraction_tilt_angle.num_images _item_description.description ; the number of images measured at the specified tilt angle. ; _item.name '_em_electron_diffraction_tilt_angle.num_images' _item.category_id em_electron_diffraction_tilt_angle _item.mandatory_code no _item_type.code int _item_examples.case '51' save_ ################################### ## EM_ELECTRON_DIFFRACTION_SHELL ## ################################### save_em_electron_diffraction_shell _category.description ; data items in the em_electron_diffraction_shell category record details about the quality of the phase information within a specified resolution range. ; _category.id em_electron_diffraction_shell _category.mandatory_code no loop_ _category_key.name '_em_electron_diffraction_shell.id' '_em_electron_diffraction_shell.electron_diffraction_id' loop_ _category_group.id 'inclusive_group' 'em_group' 'em_data_collection_group' 'em_2D_crystal_group' loop_ _category_examples.detail _category_examples.case ; based on pdb entry 1TUB ; ; loop_ _em_electron_diffraction_shell.electron_diffraction_id _em_electron_diffraction_shell.id _em_electron_diffraction_shell.d_res_low _em_electron_diffraction_shell.d_res_high _em_electron_diffraction_shell.residual 1 1 5.0 4.0 36 1 2 4.0 3.7 46 ; save_ save__em_electron_diffraction_shell.electron_diffraction_id _item_description.description ; this data item is a pointer to _em_electron_diffraction.id in the em_electron_diffraction category. ; _item.name '_em_electron_diffraction_shell.electron_diffraction_id' _item.category_id em_electron_diffraction_shell _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_electron_diffraction_shell.electron_diffraction_id' _item_linked.parent_name '_em_electron_diffraction.id' save_ save__em_electron_diffraction_shell.id _item_description.description ; the value of _electron_diffraction_shell.id must uniquely identify a resolution range of the electron diffraction data. ; _item.name '_em_electron_diffraction_shell.id' _item.category_id em_electron_diffraction_shell _item.mandatory_code yes _item_type.code code save_ save__em_electron_diffraction_shell.d_res_low _item_description.description ; the lowest resolution d-value for the resolution range. ; _item.name '_em_electron_diffraction_shell.d_res_low' _item.category_id em_electron_diffraction_shell _item.mandatory_code no _item_type.code int _item_examples.case '4.0' save_ save__em_electron_diffraction_shell.d_res_high _item_description.description ; the highest resolution d-value for the resolution range. ; _item.name '_em_electron_diffraction_shell.d_res_high' _item.category_id em_electron_diffraction_shell _item.mandatory_code no _item_type.code int _item_examples.case '5.0' save_ save__em_electron_diffraction_shell.residual _item_description.description ; the phase residual value for the electron diffraction experiment. ; _item.name '_em_electron_diffraction_shell.residual' _item.category_id em_electron_diffraction_shell _item.mandatory_code no _item_type.code int save_ ################################# ## EM_EULER_ANGLE_DISTRIBUTION ## ################################# # #save_em_euler_angle_distribution # _category.description #; Data items in the EM_EULER_ANGLE_DISTRIBUTION category # record details of assignment of Euler angles for projection # sets of particles. #; # _category.id em_euler_angle_distribution # _category.mandatory_code no # loop_ # _category_key.name # '_em_euler_angle_distribution.id' # '_em_euler_angle_distribution.entry_id' # loop_ # _category_group.id 'inclusive_group' # 'em_group' # loop_ # _category_examples.detail # _category_examples.case #; Example 1 - based on PDB entry 1DYL and laboratory records for the # structure corresponding to PDB entry 1DYL #; #; # _em_euler_angle_distribution.entry_id 1DYL # _em_euler_angle_distribution.id 1 # _em_euler_angle_distribution.details . # _em_euler_angle_distribution.alpha . # _em_euler_angle_distribution.beta . # _em_euler_angle_distribution.gamma . #; # save_ # #save__em_euler_angle_distribution.id # _item_description.description #; The value of _em_euler_angle_distribution.id must # uniquely identify the euler angle assignments of # the projection set used in the final reconstruction. #; # _item.name '_em_euler_angle_distribution.id' # _item.category_id em_euler_angle_distribution # _item.mandatory_code yes # _item_type.code code # save_ # #save__em_euler_angle_distribution.entry_id # _item_description.description #; The value of _entry.id is a pointer # to the ENTRY category. #; # _item.name '_em_euler_angle_distribution.entry_id' # _item.category_id em_euler_angle_distribution # _item.mandatory_code yes # _item_type.code code # _item_linked.child_name '_em_euler_angle_distribution.entry_id' # _item_linked.parent_name '_entry.id' # save_ # # #save__em_euler_angle_distribution.details # _item_description.description #; Any additional details of the euler angles distribution and assignment. #; # _item.name '_em_euler_angle_distribution.details' # _item.category_id em_euler_angle_distribution # _item.mandatory_code no # _item_type.code text # save_ # #save__em_euler_angle_distribution.alpha # _item_description.description #; The euler-alpha angle assignment. #; # _item.name '_em_euler_angle_distribution.alpha' # _item.category_id em_euler_angle_distribution # _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_examples.case 90 # save_ # #save__em_euler_angle_distribution.beta # _item_description.description #; The euler-beta angle assignment. #; # _item.name '_em_euler_angle_distribution.beta' # _item.category_id em_euler_angle_distribution # _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_examples.case 90 # save_ # #save__em_euler_angle_distribution.gamma # _item_description.description #; The euler-gamma angle assignment. #; # _item.name '_em_euler_angle_distribution.gamma' # _item.category_id em_euler_angle_distribution # _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_examples.case 0 # save_ # ####################### ## BUFFER_COMPONENTS ## ####################### # #save_BUFFER_COMPONENTS # _category.description #; Constituents of buffer in sample #; # _category.id buffer_components # _category.mandatory_code no # loop_ # _category_key.name # '_buffer_components.buffer_id' # '_buffer_components.id' # loop_ # _category_group.id 'inclusive_group' # 'em_group' # loop_ # _category_examples.detail # _category_examples.case #; Example 1 - based on PDB entry 1DYL and laboratory records for the # structure corresponding to PDB entry 1DYL #; #;loop_ # _buffer_components.buffer_id # _buffer_components.id # _buffer_components.name # _buffer_components.volume # _buffer_components.conc # _buffer_components.details # 1 1 'NaCl' '0.200 ' '4 ' . # 1 2 'Acetic Acid' '0.047 ' '100' . # 1 3 'water' '0.700 ' 'neat' . #; # save_ # # #save__buffer_components.id # _item_description.description #; The value of _buffer_components.id must # uniquely identify a component of the buffer. #; # _item.name '_buffer_components.id' # _item.category_id buffer_components # _item.mandatory_code yes # _item_type.code code # save_ # # #save__buffer_components.buffer_id # _item_description.description #; This data item is a pointer to _buffer.id in the BUFFER category. #; # _item.name '_buffer_components.buffer_id' # _item.category_id buffer_components # _item.mandatory_code yes # _item_type.code code # save_ # #save__buffer_components.name # _item_description.description #; The name of each buffer component. #; # _item.name '_buffer_components.name' # _item.category_id buffer_components # _item.mandatory_code no # _item_type.code line # _item_examples.case 'Acetic acid' # save_ # #save__buffer_components.volume # _item_description.description #; The volume of buffer component. #; # _item.name '_buffer_components.volume' # _item.category_id buffer_components # _item.mandatory_code no # _item_type.code code # _item_examples.case 0.200 # save_ # #save__buffer_components.conc # _item_description.description #; The millimolar concentration of buffer component. #; # _item.name '_buffer_components.conc' # _item.category_id buffer_components # _item.mandatory_code no # _item_type.code code # _item_examples.case 200 # save_ # #save__buffer_components.details # _item_description.description #; Any additional details to do with buffer composition. #; # _item.name '_buffer_components.details' # _item.category_id buffer_components # _item.mandatory_code no # _item_type.code text # _item_examples.case 'pH adjusted with NaOH' # save_ # ## EOF - mmcif_em-def-1.dic # loop_ _pdbx_item_linked_group.category_id _pdbx_item_linked_group.link_group_id _pdbx_item_linked_group.label _pdbx_item_linked_group.context _pdbx_item_linked_group.condition_id em_2d_crystal_entity 1 em_2d_crystal_entity:em_entity_assembly:1 . . em_2d_crystal_selection 1 em_2d_crystal_selection:em_particle_selection:1 . . em_3d_fitting 1 em_3d_fitting:entry:1 . . em_3d_fitting_list 1 em_3d_fitting_list:em_3d_fitting:1 . . em_3d_fitting_list 2 em_3d_fitting_list:entry:2 . . em_3d_fitting_list 3 em_3d_fitting_list:entry:3 . . em_3d_fitting_list 4 em_3d_fitting_list:entry:4 . . em_3d_reconstruction 1 em_3d_reconstruction:citation:1 . . em_3d_reconstruction 2 em_3d_reconstruction:entry:2 . . em_3d_refinement 1 em_3d_refinement:entry:1 . . em_array_formation 1 em_array_formation:citation:1 . . em_array_formation 2 em_array_formation:em_solution_composition:2 . . em_assembly 1 em_assembly:entry:1 . . em_classes 1 em_classes:entry:1 . . em_cryo_stain 1 em_cryo_stain:em_sample_preparation:1 . . em_cryo_stain 2 em_cryo_stain:entry:2 . . em_detector 1 em_detector:entry:1 . . em_detector_CCD 1 em_detector_CCD:em_detector:1 . . em_detector_film 1 em_detector_film:em_detector:1 . . em_electron_diffraction 1 em_electron_diffraction:entry:1 . . em_electron_diffraction_shell 1 em_electron_diffraction_shell:em_electron_diffraction:1 . . em_electron_diffraction_tilt_angle 1 em_electron_diffraction_tilt_angle:em_electron_diffraction:1 . . em_embedding_agent 1 em_embedding_agent:entry:1 . . em_entity_assembly 1 em_entity_assembly:em_assembly:1 . . em_entity_assembly_list 1 em_entity_assembly_list:em_assembly:1 . . em_entity_assembly_list 2 em_entity_assembly_list:entity:2 . . em_entity_assembly_mol_wt 1 em_entity_assembly_mol_wt:em_entity_assembly:1 . . em_entity_assembly_mol_wt 2 em_entity_assembly_mol_wt:em_entity_assembly_list:2 . . em_exptl 1 em_exptl:entry:1 . . em_helical_entity 1 em_helical_entity:em_entity_assembly:1 . . em_helical_selection 1 em_helical_selection:em_particle_selection:1 . . em_image_readout_ccd 1 em_image_readout_ccd:em_image_scanning:1 . . em_image_scanning 1 em_image_scanning:citation:1 . . em_image_scanning 2 em_image_scanning:entry:2 . . em_image_scanning_film 1 em_image_scanning_film:em_image_scanning:1 . . em_imaging 1 em_imaging:citation:1 . . em_imaging 2 em_imaging:em_detector:2 . . em_imaging 3 em_imaging:em_image_scanning:3 . . em_imaging 4 em_imaging:em_microscope:4 . . em_imaging 5 em_imaging:em_sample_support:5 . . em_imaging 6 em_imaging:entry:6 . . em_map 1 em_map:em_3d_reconstruction:1 . . em_map 2 em_map:em_imaging:2 . . em_map 3 em_map:em_map_files:3 . . em_map 4 em_map:em_map_structure_factors:4 . . em_map 5 em_map:em_map_symmetry:5 . . em_map 6 em_map:entry:6 . . em_map_ctf_correction 1 em_map_ctf_correction:em_map:1 . . em_map_eigenvalues 1 em_map_eigenvalues:em_map:1 . . em_map_figure 1 em_map_figure:em_map:1 . . em_map_files 1 em_map_files:em_map:1 . . em_map_resolution 1 em_map_resolution:em_fsc_curve:1 . . em_map_resolution 2 em_map_resolution:em_map:2 . . em_map_resolution 3 em_map_resolution:entry:3 . . em_map_structure_factors 1 em_map_structure_factors:em_map:1 . . em_map_structure_factors 2 em_map_structure_factors:em_map_files:2 . . em_map_surface_rendering 1 em_map_surface_rendering:em_map:1 . . em_map_surface_rendering 2 em_map_surface_rendering:em_map_files:2 . . em_map_symmetry 1 em_map_symmetry:em_map:1 . . em_micrographs 1 em_micrographs:em_microscope:1 . . em_micrographs 2 em_micrographs:em_sample_preparation:2 . . em_micrographs 3 em_micrographs:entry:3 . . em_orthogonal_slices 1 em_orthogonal_slices:em_map:1 . . em_particle_selection 1 em_particle_selection:citation:1 . . em_particle_selection 2 em_particle_selection:em_entity_assembly:2 . . em_sample_preparation 1 em_sample_preparation:em_entity_assembly:1 . . em_sample_preparation 2 em_sample_preparation:em_sample_support:2 . . em_sample_preparation 3 em_sample_preparation:em_solution_composition:3 . . em_sample_support 1 em_sample_support:citation:1 . . em_single_particle_entity 1 em_single_particle_entity:em_entity_assembly:1 . . em_single_particle_selection 1 em_single_particle_selection:citation:1 . . em_single_particle_selection 2 em_single_particle_selection:em_particle_selection:2 . . em_stain 1 em_stain:em_sample_preparation:1 . . em_stain 2 em_stain:entry:2 . . em_tomography 1 em_tomography:entry:1 . . em_virus_entity 1 em_virus_entity:em_entity_assembly:1 . . em_virus_shells 1 em_virus_shells:em_virus_entity:1 . . em_vitrification 1 em_vitrification:citation:1 . . em_vitrification 2 em_vitrification:em_sample_preparation:2 . . em_vitrification 3 em_vitrification:entry:3 . . # loop_ _pdbx_item_linked_group_list.child_category_id _pdbx_item_linked_group_list.link_group_id _pdbx_item_linked_group_list.child_name _pdbx_item_linked_group_list.parent_name _pdbx_item_linked_group_list.parent_category_id em_2d_crystal_entity 1 '_em_2d_crystal_entity.entity_assembly_id' '_em_entity_assembly.id' em_entity_assembly em_2d_crystal_selection 1 '_em_2d_crystal_selection.selection_id' '_em_particle_selection.id' em_particle_selection em_3d_fitting 1 '_em_3d_fitting.entry_id' '_entry.id' entry em_3d_fitting_list 1 '_em_3d_fitting_list.3d_fitting_id' '_em_3d_fitting.id' em_3d_fitting em_3d_fitting_list 2 '_em_3d_fitting_list.pdb_entry_id' '_entry.id' entry em_3d_fitting_list 3 '_em_3d_fitting_list.fitted_pdb_entry_id' '_entry.id' entry em_3d_fitting_list 4 '_em_3d_fitting_list.entry_id' '_entry.id' entry em_3d_reconstruction 1 '_em_3d_reconstruction.citation_id' '_citation.id' citation em_3d_reconstruction 2 '_em_3d_reconstruction.entry_id' '_entry.id' entry em_3d_refinement 1 '_em_3d_refinement.entry_id' '_entry.id' entry em_array_formation 1 '_em_array_formation.citation_id' '_citation.id' citation em_array_formation 2 '_em_array_formation.buffer_id' '_em_solution_composition.id' em_solution_composition em_assembly 1 '_em_assembly.entry_id' '_entry.id' entry em_classes 1 '_em_classes.entry_id' '_entry.id' entry em_cryo_stain 1 '_em_cryo_stain.sample_preparation_id' '_em_sample_preparation.id' em_sample_preparation em_cryo_stain 2 '_em_cryo_stain.entry_id' '_entry.id' entry em_detector 1 '_em_detector.entry_id' '_entry.id' entry em_detector_CCD 1 '_em_detector_CCD.detector_id' '_em_detector.id' em_detector em_detector_film 1 '_em_detector_film.detector_id' '_em_detector.id' em_detector em_electron_diffraction 1 '_em_electron_diffraction.entry_id' '_entry.id' entry em_electron_diffraction_shell 1 '_em_electron_diffraction_shell.electron_diffraction_id' '_em_electron_diffraction.id' em_electron_diffraction em_electron_diffraction_tilt_angle 1 '_em_electron_diffraction_tilt_angle.electron_diffraction_id' '_em_electron_diffraction.id' em_electron_diffraction em_embedding_agent 1 '_em_embedding_agent.entry_id' '_entry.id' entry em_entity_assembly 1 '_em_entity_assembly.assembly_id' '_em_assembly.id' em_assembly em_entity_assembly_list 1 '_em_entity_assembly_list.assembly_id' '_em_assembly.id' em_assembly em_entity_assembly_list 2 '_em_entity_assembly_list.entity_id' '_entity.id' entity em_entity_assembly_mol_wt 1 '_em_entity_assembly_mol_wt.entity_assembly_id' '_em_entity_assembly.id' em_entity_assembly em_entity_assembly_mol_wt 2 '_em_entity_assembly_mol_wt.id' '_em_entity_assembly_list.id' em_entity_assembly_list em_exptl 1 '_em_exptl.entry_id' '_entry.id' entry em_helical_entity 1 '_em_helical_entity.entity_assembly_id' '_em_entity_assembly.id' em_entity_assembly em_helical_selection 1 '_em_helical_selection.selection_id' '_em_particle_selection.id' em_particle_selection em_image_readout_ccd 1 '_em_image_readout_ccd.image_scanning_id' '_em_image_scanning.id' em_image_scanning em_image_scanning 1 '_em_image_scanning.citation_id' '_citation.id' citation em_image_scanning 2 '_em_image_scanning.entry_id' '_entry.id' entry em_image_scanning_film 1 '_em_image_scanning_film.image_scanning_id' '_em_image_scanning.id' em_image_scanning em_imaging 1 '_em_imaging.citation_id' '_citation.id' citation em_imaging 2 '_em_imaging.detector_id' '_em_detector.id' em_detector em_imaging 3 '_em_imaging.image_scanning_id' '_em_image_scanning.id' em_image_scanning em_imaging 4 '_em_imaging.microscope_id' '_em_microscope.id' em_microscope em_imaging 5 '_em_imaging.sample_support_id' '_em_sample_support.id' em_sample_support em_imaging 6 '_em_imaging.entry_id' '_entry.id' entry em_map 1 '_em_map.3d_reconstruction_id' '_em_3d_reconstruction.id' em_3d_reconstruction em_map 2 '_em_map.imaging_id' '_em_imaging.id' em_imaging em_map 3 '_em_map.map_files_id' '_em_map_files.id' em_map_files em_map 4 '_em_map.map_structure_factors_id' '_em_map_structure_factors.id' em_map_structure_factors em_map 5 '_em_map.map_symmetry_id' '_em_map_symmetry.id' em_map_symmetry em_map 6 '_em_map.entry_id' '_entry.id' entry em_map_ctf_correction 1 '_em_map_ctf_correction.map_id' '_em_map.id' em_map em_map_eigenvalues 1 '_em_map_eigenvalues.map_id' '_em_map.id' em_map em_map_figure 1 '_em_map_figure.map_id' '_em_map.id' em_map em_map_files 1 '_em_map_files.map_id' '_em_map.id' em_map em_map_resolution 1 '_em_map_resolution.curve_id' '_em_fsc_curve.curve_id' em_fsc_curve em_map_resolution 2 '_em_map_resolution.map_id' '_em_map.id' em_map em_map_resolution 3 '_em_map_resolution.entry_id' '_entry.id' entry em_map_structure_factors 1 '_em_map_structure_factors.map_id' '_em_map.id' em_map em_map_structure_factors 2 '_em_map_structure_factors.map_files_id' '_em_map_files.id' em_map_files em_map_surface_rendering 1 '_em_map_surface_rendering.map_id' '_em_map.id' em_map em_map_surface_rendering 2 '_em_map_surface_rendering.map_files_id' '_em_map_files.id' em_map_files em_map_symmetry 1 '_em_map_symmetry.map_id' '_em_map.id' em_map em_micrographs 1 '_em_micrographs.microscope_id' '_em_microscope.id' em_microscope em_micrographs 2 '_em_micrographs.specimen_id' '_em_sample_preparation.id' em_sample_preparation em_micrographs 3 '_em_micrographs.entry_id' '_entry.id' entry em_orthogonal_slices 1 '_em_orthogonal_slices.map_id' '_em_map.id' em_map em_particle_selection 1 '_em_particle_selection.citation_id' '_citation.id' citation em_particle_selection 2 '_em_particle_selection.entity_assembly_id' '_em_entity_assembly.id' em_entity_assembly em_sample_preparation 1 '_em_sample_preparation.entity_assembly_id' '_em_entity_assembly.id' em_entity_assembly em_sample_preparation 2 '_em_sample_preparation.support_id' '_em_sample_support.id' em_sample_support em_sample_preparation 3 '_em_sample_preparation.solution_id' '_em_solution_composition.id' em_solution_composition em_sample_support 1 '_em_sample_support.citation_id' '_citation.id' citation em_single_particle_entity 1 '_em_single_particle_entity.entity_assembly_id' '_em_entity_assembly.id' em_entity_assembly em_single_particle_selection 1 '_em_single_particle_selection.citation_id' '_citation.id' citation em_single_particle_selection 2 '_em_single_particle_selection.selection_id' '_em_particle_selection.id' em_particle_selection em_stain 1 '_em_stain.sample_preparation_id' '_em_sample_preparation.id' em_sample_preparation em_stain 2 '_em_stain.entry_id' '_entry.id' entry em_tomography 1 '_em_tomography.entry_id' '_entry.id' entry em_virus_entity 1 '_em_virus_entity.entity_assembly_id' '_em_entity_assembly.id' em_entity_assembly em_virus_shells 1 '_em_virus_shells.virus_entity_id' '_em_virus_entity.id' em_virus_entity em_vitrification 1 '_em_vitrification.citation_id' '_citation.id' citation em_vitrification 2 '_em_vitrification.sample_preparation_id' '_em_sample_preparation.id' em_sample_preparation em_vitrification 3 '_em_vitrification.entry_id' '_entry.id' entry #