PDBML 4-0 Reference

OVERVIEW

Tree Structure

DETAILS

Attributes

_3d_fitting_id

action_type

align_id

alt_id

assembly_id

assigned_chem_shift_list_id

asym_id

asym_id_list

atom_1

atom_1_valence

atom_2

atom_2_valence

atom_id

atom_id_1

atom_id_2

atom_id_3

atom_isotope_number

atom_site_id_1

atom_site_id_2

atom_site_id_3

atom_site_id_4

atom_site_id_A

atom_site_id_D

atom_site_id_H

atom_type

atom_type_1

atom_type_2

beg_label_alt_id

beg_label_asym_id

beg_label_comp_id

beg_label_seq_id

biol_id

block_code

block_description

buffer_id

chem_shift_reference_id

chir_id

citation_id

class

clust_id

code

comp_id

component

component_id

conditions_id

constraint_filename

constraint_subtype

constraint_type

construct_id

content_type

coord_section

crystal_id

cycle_id

d_res_high

d_res_low

data_file_id

database_code

database_id

datablockName

date

db_id

db_name

der_id

dict_name

dict_version

diffrn_id

dom_id

dom_id_1

dom_id_2

domain_id

edit_op

element

end_label_alt_id

end_label_asym_id

end_label_comp_id

end_label_seq_id

ens_id

entity_assembly_id

entity_id

entity_inst_id

entry_id

experiment_id

expt_id

family_prd_id

feature

feature_id

feature_type

group_code

hetero

i_label_asym_id

i_label_asym_id_1

i_label_asym_id_2

i_label_comp_id

i_label_comp_id_1

i_label_comp_id_2

i_label_seq_id

i_label_seq_id_1

i_label_seq_id_2

i_symmetry

i_symmetry_1

i_symmetry_2

id

index_h

index_k

index_l

instance_id

j_label_asym_id

j_label_asym_id_1

j_label_asym_id_2

j_label_comp_id

j_label_comp_id_1

j_label_comp_id_2

j_label_seq_id

j_label_seq_id_1

j_label_seq_id_2

j_symmetry

j_symmetry_1

j_symmetry_2

label

label_alt_id

label_asym_id

label_comp_id

label_seq_id

major_version

message_id

method

minor_version

model_number

mol_common_name

mon_id

msym_id

name

name_type

ndb_seq_num

num

number

oper_expression

oper_id

operator

ordinal

parameter

pdb_id

pdbx_component_id

pdbx_ens_id

pdbx_id

pdbx_ordinal

pdbx_refine_id

plane_id

prd_id

program

program_version

property_id

protocol_type

publication_abbrev

range_id_1

range_id_2

ref_entity_id

replace_pdb_id

rev_num

revision_id

revision_type

scatter_id

seq

seq_id

seq_range_id

serial

serial_no

set_id

sheet_id

site_id

site_symmetry_1

site_symmetry_2

site_symmetry_3

site_symmetry_4

site_symmetry_A

site_symmetry_D

site_symmetry_H

software_id

software_ordinal

sol_id

solution_id

source

spectral_peak_list_id

spectral_region

spectrometer_id

step_id

struct_group_id

symbol

symmetry

task

term

text

tls_group_id

tor_id

type

units

value

virus_entity_id

wavelength

wavelength_1

wavelength_2

Elements

_2d_crystal_grow_id

A_calc

A_calc_au

A_meas

A_meas_au

absolute_configuration

absorpt_coefficient_mu

absorpt_correction_T_max

absorpt_correction_T_min

absorpt_correction_type

absorpt_process_details

abstract

abstract_id_CAS

accelerating_voltage

actual_pixel_size

address

address_1

address_2

address_3

adp_type

aggregation_state

align_id

alpha

alt_atom_id

ambient_environment

ambient_pressure

ambient_pressure_esd

ambient_pressure_gt

ambient_pressure_lt

ambient_temp

ambient_temp_details

ambient_temp_esd

ambient_temp_gt

ambient_temp_lt

analytical

analytical_mass_percent

angle

angle_alpha

angle_alpha_esd

angle_beta

angle_beta_esd

angle_chi

angle_deviation

angle_DHA

angle_DHA_esd

angle_esd

angle_gamma

angle_gamma_esd

angle_kappa

angle_omega

angle_phi

angle_psi

angle_standard_deviation

angle_target_value

angle_theta

angle_value

angular_rotation_per_subunit

aniso_B11

aniso_B11_esd

aniso_B12

aniso_B12_esd

aniso_B13

aniso_B13_esd

aniso_B22

aniso_B22_esd

aniso_B23

aniso_B23_esd

aniso_B33

aniso_B33_esd

aniso_ratio

aniso_U11

aniso_U11_esd

aniso_U12

aniso_U12_esd

aniso_U13

aniso_U13_esd

aniso_U22

aniso_U22_esd

aniso_U23

aniso_U23_esd

aniso_U33

aniso_U33_esd

annealing_details

annotator

apparatus

area_resol_mean

assembly_id

astigmatism

ASTM_code_type

ASTM_code_value

asym_id

atcc

atmosphere

atom_1_comp_id

atom_2_comp_id

atom_3_comp_id

atom_4_comp_id

atom_comp_id

atom_config

atom_deviation

atom_group

atom_id

atom_id_1

atom_id_2

atom_id_3

atom_id_4

atom_isotope_number

atom_site

atom_site_anisotrop

atom_site_anisotropCategory

atom_site_auth_asym_id_1

atom_site_auth_asym_id_2

atom_site_auth_asym_id_3

atom_site_auth_asym_id_4

atom_site_auth_asym_id_A

atom_site_auth_asym_id_D

atom_site_auth_asym_id_H

atom_site_auth_atom_id_1

atom_site_auth_atom_id_2

atom_site_auth_atom_id_3

atom_site_auth_atom_id_4

atom_site_auth_atom_id_A

atom_site_auth_atom_id_D

atom_site_auth_atom_id_H

atom_site_auth_comp_id_1

atom_site_auth_comp_id_2

atom_site_auth_comp_id_3

atom_site_auth_comp_id_4

atom_site_auth_comp_id_A

atom_site_auth_comp_id_D

atom_site_auth_comp_id_H

atom_site_auth_seq_id_1

atom_site_auth_seq_id_2

atom_site_auth_seq_id_3

atom_site_auth_seq_id_4

atom_site_auth_seq_id_A

atom_site_auth_seq_id_D

atom_site_auth_seq_id_H

atom_site_label_alt_id_1

atom_site_label_alt_id_2

atom_site_label_alt_id_3

atom_site_label_alt_id_4

atom_site_label_alt_id_A

atom_site_label_alt_id_D

atom_site_label_alt_id_H

atom_site_label_asym_id_1

atom_site_label_asym_id_2

atom_site_label_asym_id_3

atom_site_label_asym_id_4

atom_site_label_asym_id_A

atom_site_label_asym_id_D

atom_site_label_asym_id_H

atom_site_label_atom_id_1

atom_site_label_atom_id_2

atom_site_label_atom_id_3

atom_site_label_atom_id_4

atom_site_label_atom_id_A

atom_site_label_atom_id_D

atom_site_label_atom_id_H

atom_site_label_comp_id_1

atom_site_label_comp_id_2

atom_site_label_comp_id_3

atom_site_label_comp_id_4

atom_site_label_comp_id_A

atom_site_label_comp_id_D

atom_site_label_comp_id_H

atom_site_label_seq_id_1

atom_site_label_seq_id_2

atom_site_label_seq_id_3

atom_site_label_seq_id_4

atom_site_label_seq_id_A

atom_site_label_seq_id_D

atom_site_label_seq_id_H

atom_siteCategory

atom_sites

atom_sites_alt

atom_sites_alt_ens

atom_sites_alt_ensCategory

atom_sites_alt_gen

atom_sites_alt_genCategory

atom_sites_altCategory

atom_sites_footnote

atom_sites_footnoteCategory

atom_sitesCategory

atom_type

atom_type_symbol

atom_typeCategory

attached_hydrogens

attenuator_code

audit

audit_author

audit_authorCategory

audit_conform

audit_conformCategory

audit_contact_author

audit_contact_authorCategory

audit_linkCategory

auditCategory

auth_alt_id

auth_asym_id

auth_asym_id_1

auth_asym_id_2

auth_asym_id_3

auth_asym_id_list

auth_atom_id

auth_atom_id_1

auth_atom_id_2

auth_atom_id_3

auth_comp_id

auth_comp_id_1

auth_comp_id_2

auth_comp_id_3

auth_mon_id

auth_seq_id

auth_seq_id_1

auth_seq_id_2

auth_seq_id_3

auth_seq_num

author_approval_type

author_name

author_release_status_code

authors

av_R_eq

av_R_equivalents

av_sgI_over_I

av_sigmaI_over_netI

av_uI_over_I

av_unetI_over_netI

average_constraint_violations_per_residue

average_constraints_per_residue

average_distance_constraint_violation

average_torsion_angle_constraint_violation

axial_rise_per_subunit

axial_symmetry

B

B11

B11_esd

B12

B12_esd

B13

B13_esd

B22

B22_esd

B23

B23_esd

B33

B33_esd

B_calc

B_calc_au

B_equiv_geom_mean

B_equiv_geom_mean_esd

b_iso

B_iso

b_iso_esd

B_iso_esd

B_iso_main_chain

B_iso_max

B_iso_mean

B_iso_min

B_iso_or_equiv

B_iso_or_equiv_esd

B_iso_side_chain

B_iso_Wilson_estimate

B_meas

B_meas_au

beg_auth_asym_id

beg_auth_comp_id

beg_auth_mon_id

beg_auth_seq_id

beg_db_mon_id

beg_db_seq_id

beg_label_alt_id

beg_label_asym_id

beg_label_comp_id

beg_label_seq_id

beg_PDB_ins_code

beg_pdb_ins_code

beg_seq_num

beta

biol_id

bond_angle_rms_dev

bond_angle_rms_dev_error

bond_deviation

bond_standard_deviation

bond_target_value

bond_value

book_id_ISBN

book_publisher

book_publisher_city

book_title

buckle

buffer_id

buffer_name

buffer_volume

C_terminal_seq_tag

calc_attached_atom

calc_flag

calibrated_magnification

carbon_shifts_flag

Cartn_transf_matrix11

Cartn_transf_matrix12

Cartn_transf_matrix13

Cartn_transf_matrix21

Cartn_transf_matrix22

Cartn_transf_matrix23

Cartn_transf_matrix31

Cartn_transf_matrix32

Cartn_transf_matrix33

Cartn_transf_vector1

Cartn_transf_vector2

Cartn_transf_vector3

Cartn_transform_axes

Cartn_x

Cartn_x_esd

Cartn_y

Cartn_y_esd

Cartn_z

Cartn_z_esd

cell

cell_angle_alpha

cell_angle_beta

cell_angle_gamma

cell_length_a

cell_length_b

cell_length_c

cell_measurement

cell_measurement_refln

cell_measurement_reflnCategory

cell_measurementCategory

cell_refinement

cell_setting

cellCategory

chain_range_begin

chain_range_end

charge

chem_comp

chem_comp_angle

chem_comp_angleCategory

chem_comp_atom

chem_comp_atomCategory

chem_comp_bond

chem_comp_bondCategory

chem_comp_chir

chem_comp_chir_atom

chem_comp_chir_atomCategory

chem_comp_chirCategory

chem_comp_id

chem_comp_linkCategory

chem_comp_plane

chem_comp_plane_atom

chem_comp_plane_atomCategory

chem_comp_planeCategory

chem_comp_tor

chem_comp_tor_value

chem_comp_tor_valueCategory

chem_comp_torCategory

chem_compCategory

chem_linkCategory

chem_shift_13C_err

chem_shift_15N_err

chem_shift_19F_err

chem_shift_1H_err

chem_shift_2H_err

chem_shift_31P_err

chem_shift_reference_id

chem_shift_units

chem_shift_val

chemical

chemical_conn_atom

chemical_conn_atomCategory

chemical_conn_bond

chemical_conn_bondCategory

chemical_conn_number

chemical_formula

chemical_formulaCategory

chemicalCategory

chi1

chi2

chi3

chi4

chi5

chi_squared

circular_symmetry

citation

citation_author

citation_authorCategory

citation_editor

citation_editorCategory

citation_id

citationCategory

city

class

class_code

class_evidence_code

classification

cleavage_buffer_id

cleavage_enzymes

cleavage_temperature

cleavage_time

code

code_CAS

code_CSD

code_depnum_ccdc_archive

code_depnum_ccdc_fiz

code_depnum_ccdc_journal

code_ICSD

code_MDF

code_NBS

code_PDB

code_PDF

coden_ASTM

coden_Cambridge

coeditor_address

coeditor_code

coeditor_email

coeditor_fax

coeditor_name

coeditor_notes

coeditor_phone

collimation

colour

colour_lustre

colour_modifier

colour_primary

column_temperature

column_type

column_volume

common_name

comp_id

comp_id_1

comp_id_2

comp_name

compiler_name

compiler_version

component_1

component_2

composition

compound_details

compound_source

computing

computingCategory

conc

conc_assay_method

conc_details

conc_device_id

conc_range

conc_units

concentration

concentration_range

concentration_units

conditions_id

conditions_label

conf_type_id

conformer_id

conformer_selection_criteria

conformers_calculated_total_number

conformers_submitted_total_number

conn_type_id

connect

constraint_number

constraints

contact_author

contact_author_address

contact_author_email

contact_author_fax

contact_author_name

contact_author_phone

contact_letter

content_type

contents

continent

cooling_details

coord_average_rmsd_method

coordinate_linkage

correction_val

correlation

correlation_coeff_Fo_to_Fc

correlation_coeff_Fo_to_Fc_free

correlation_coeff_Io_to_Ic

correlation_main_chain

correlation_side_chain

country

counts_bg_1

counts_bg_2

counts_net

counts_peak

counts_total

covalent_bond_rms_dev

covalent_bond_rms_dev_error

covalent_geom_angles_term

covalent_geom_angles_term_units

covalent_geom_bond_term

covalent_geom_bond_term_units

covalent_geom_impropers_term

covalent_geom_impropers_term_units

creation_date

creation_method

criteria

criterion

cryogen_name

crystal_id

crystal_support

crystal_system

crystal_treatment

crystals_number

CSD_history

ctf_correction_method

culture_additives

culture_base_media

culture_temperature

culture_time

culture_volume

current

current_version

d_res_high

d_res_high_rotation

d_res_high_translation

d_res_low

d_res_low_rotation

d_res_low_translation

d_resolution_high

d_resolution_low

d_spacing

data_analysis_software_list

data_collection

data_file_category

data_file_name

data_file_syntax

data_reduction

data_reduction_details

data_reduction_method

data_reduction_software_list

data_reference

data_set_type

data_validation_number

database

database_2

database_2Category

database_id_CSD

database_id_Medline

database_PDB_caveat

database_PDB_caveatCategory

database_PDB_matrix

database_PDB_matrixCategory

database_PDB_remark

database_PDB_remarkCategory

database_PDB_rev

database_PDB_rev_record

database_PDB_rev_recordCategory

database_PDB_revCategory

database_PDB_tvect

database_PDB_tvectCategory

databaseCategory

datablock

date

date_accepted

date_author_approval

date_author_release_request

date_begin_cycle

date_begin_deposition

date_begin_processing

date_begin_release_preparation

date_chemical_shifts

date_coordinates

date_deposition_form

date_end_cycle

date_end_processing

date_from_coeditor

date_hold_chemical_shifts

date_hold_coordinates

date_hold_nmr_constraints

date_hold_struct_fact

date_manuscript

date_nmr_constraints

date_of_cs_release

date_of_mr_release

date_of_PDB_release

date_of_sf_release

date_original

date_printers_final

date_printers_first

date_proofs_in

date_proofs_out

date_recd_electronic

date_recd_hard_copy

date_struct_fact

date_submitted

date_to_coeditor

db_accession

db_align_beg

db_align_end

db_code

db_mon_id

db_name

db_seq_id

decay_

delta

delta_delta_phi

delta_phi

delta_phi_final

delta_phi_initial

delta_phi_sigma

denature_buffer_id

density_diffrn

density_index

density_index_main_chain

density_index_side_chain

density_Matthews

density_meas

density_meas_esd

density_meas_gt

density_meas_lt

density_meas_temp

density_meas_temp_esd

density_meas_temp_gt

density_meas_temp_lt

density_method

density_percent_sol

density_ratio

density_ratio_main_chain

density_ratio_side_chain

dep_release_code_chemical_shifts

dep_release_code_coordinates

dep_release_code_nmr_constraints

dep_release_code_sequence

dep_release_code_struct_fact

dependencies

deposit_site

der_set_id

description

descriptor

details

detect_slit_horiz

detect_slit_vert

detective_quantum_efficiency

detector

detector_distance

detector_id

detector_specific

detector_type

dev

dev_ideal

dev_ideal_target

device

device_details

device_type

dict_location

diff_density_max

diff_density_max_esd

diff_density_min

diff_density_min_esd

diff_density_rms

diff_density_rms_esd

diffr_chi

diffr_kappa

diffr_phi

diffr_psi

diffrn

diffrn_attenuator

diffrn_attenuatorCategory

diffrn_detector

diffrn_detectorCategory

diffrn_measurement

diffrn_measurementCategory

diffrn_orient_matrix

diffrn_orient_matrixCategory

diffrn_orient_refln

diffrn_orient_reflnCategory

diffrn_radiation

diffrn_radiation_wavelength

diffrn_radiation_wavelengthCategory

diffrn_radiationCategory

diffrn_refln

diffrn_reflnCategory

diffrn_reflns

diffrn_reflns_class

diffrn_reflns_classCategory

diffrn_reflnsCategory

diffrn_scale_group

diffrn_scale_groupCategory

diffrn_source

diffrn_sourceCategory

diffrn_standard_refln

diffrn_standard_reflnCategory

diffrn_standards

diffrn_standardsCategory

diffrnCategory

dihedral_angles_rms_dev

dihedral_angles_rms_dev_error

disorder_assembly

disorder_group

display_x

display_y

dist

dist_DA

dist_DA_esd

dist_DH

dist_DH_esd

dist_esd

dist_HA

dist_HA_esd

distance_constraint_violation_method

distance_cutoff_high

distance_cutoff_low

distance_rms_dev

distance_rms_dev_error

disulfide_bond_constraints_total_count

dom_id

domain_id

dtime

dyad

dyad_axis

ebi_cell

ebi_cellular_location

ebi_engineered

ebi_expression_system

ebi_expression_system_plasmid

ebi_organelle

ebi_organism_common

ebi_organism_scientific

ebi_strain

ebi_tissue

edit_atom_id

edit_atom_value

edit_bond_value

edit_op

elapsed_time

electron_beam_tilt_params

electron_dose

electron_source

elution_buffer_id

elution_protocol

em_2d_crystal_entity

em_2d_crystal_entityCategory

em_2d_crystal_grow

em_2d_crystal_growCategory

em_2d_projection_selection

em_2d_projection_selectionCategory

em_3d_fitting

em_3d_fitting_list

em_3d_fitting_listCategory

em_3d_fittingCategory

em_3d_reconstruction

em_3d_reconstructionCategory

em_assembly

em_assemblyCategory

em_buffer

em_buffer_components

em_buffer_componentsCategory

em_bufferCategory

em_detector

em_detectorCategory

em_electron_diffraction

em_electron_diffraction_pattern

em_electron_diffraction_patternCategory

em_electron_diffraction_phase

em_electron_diffraction_phaseCategory

em_electron_diffractionCategory

em_entity_assembly

em_entity_assembly_list

em_entity_assembly_listCategory

em_entity_assemblyCategory

em_euler_angle_distribution

em_euler_angle_distributionCategory

em_experiment

em_experimentCategory

em_helical_entity

em_helical_entityCategory

em_icos_virus_shells

em_icos_virus_shellsCategory

em_image_scans

em_image_scansCategory

em_imaging

em_imagingCategory

em_sample_preparation

em_sample_preparationCategory

em_sample_support

em_sample_supportCategory

em_single_particle_entity

em_single_particle_entityCategory

em_virus_entity

em_virus_entityCategory

em_vitrification

em_vitrificationCategory

email

empty

encoded_source_dimension_id

encoding_code

end_auth_asym_id

end_auth_comp_id

end_auth_mon_id

end_auth_seq_id

end_construct_id

end_db_mon_id

end_db_seq_id

end_label_alt_id

end_label_asym_id

end_label_comp_id

end_label_seq_id

end_PDB_ins_code

end_pdb_ins_code

end_seq

end_seq_num

end_year

energy_filter

energy_window

entity

entity_assembly_id

entity_id

entity_id_1

entity_id_2

entity_inst_id

entity_keywords

entity_keywordsCategory

entity_linkCategory

entity_name_com

entity_name_comCategory

entity_name_sys

entity_name_sysCategory

entity_poly

entity_poly_seq

entity_poly_seqCategory

entity_polyCategory

entity_seq_num_1

entity_seq_num_2

entity_src_gen

entity_src_genCategory

entity_src_nat

entity_src_natCategory

entityCategory

entry

entry_fitting_list

entry_id