XmlmmCIF equivalent: atom_site Data items in the ATOM_SITE category record details about the atom sites in a macromolecular crystal structure, such as the positional coordinates, atomic displacement parameters, magnetic moments and directions, and so on. The data items for describing anisotropic temperature or atomic displacement factors are only used if the corresponding items are not given in the ATOM_SITE_ANISOTROP category. XmlmmCIF equivalent: atom_site/B_equiv_geom_mean Equivalent isotropic atomic displacement parameter, B~equiv~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. B~equiv~ = (B~i~ B~j~ B~k~)^1/3^ B~n~ = the principal components of the orthogonalised B^ij^ The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. XmlmmCIF equivalent: atom_site/B_equiv_geom_mean_esd The estimated standard deviation of _atom_site.B_equiv_geom_mean. XmlmmCIF equivalent: atom_site/B_iso_or_equiv Isotropic temperature factor parameter, or equivalent isotropic temperature factor, B~equiv~, calculated from anisotropic temperature factor parameters. B~equiv~ = (1/3) sum~i~[sum~j~(B~ij~ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths B~ij~ = 8 pi^2^ U~ij~ Ref: Fischer, R. X. and Tillmanns, E. (1988). Acta Cryst. C44, 775-776. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. XmlmmCIF equivalent: atom_site/B_iso_or_equiv_esd The estimated standard deviation of _atom_site.B_iso_or_equiv. XmlmmCIF equivalent: atom_site/Cartn_x The x atom site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. XmlmmCIF equivalent: atom_site/Cartn_x_esd The estimated standard deviation of _atom_site.Cartn_x. XmlmmCIF equivalent: atom_site/Cartn_y The y atom site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. XmlmmCIF equivalent: atom_site/Cartn_y_esd The estimated standard deviation of _atom_site.Cartn_y. XmlmmCIF equivalent: atom_site/Cartn_z The z atom site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. XmlmmCIF equivalent: atom_site/Cartn_z_esd The estimated standard deviation of _atom_site.Cartn_z. XmlmmCIF equivalent: atom_site/U_equiv_geom_mean Equivalent isotropic atomic displacement parameter, U~equiv~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. U~equiv~ = (U~i~ U~j~ U~k~)^1/3^ U~n~ = the principal components of the orthogonalised U~ij~ XmlmmCIF equivalent: atom_site/U_equiv_geom_mean_esd The estimated standard deviation of _atom_site.U_equiv_geom_mean. XmlmmCIF equivalent: atom_site/U_iso_or_equiv Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, U~equiv~, calculated from anisotropic atomic displacement parameters. U~equiv~ = (1/3) sum~i~[sum~j~(U~ij~ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths Ref: Fischer, R. X. and Tillmanns, E. (1988). Acta Cryst. C44, 775-776. XmlmmCIF equivalent: atom_site/U_iso_or_equiv_esd The estimated standard deviation of _atom_site.U_iso_or_equiv. XmlmmCIF equivalent: atom_site/Wyckoff_symbol The Wyckoff symbol (letter) as listed in the space-group section of International Tables for Crystallography, Vol. A (1987). XmlmmCIF equivalent: atom_site/aniso_B11 The [1][1] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. XmlmmCIF equivalent: atom_site/aniso_B11_esd The estimated standard deviation of _atom_site.aniso_B[1][1]. XmlmmCIF equivalent: atom_site/aniso_B12 The [1][2] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. XmlmmCIF equivalent: atom_site/aniso_B12_esd The estimated standard deviation of _atom_site.aniso_B[1][2]. XmlmmCIF equivalent: atom_site/aniso_B13 The [1][3] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. XmlmmCIF equivalent: atom_site/aniso_B13_esd The estimated standard deviation of _atom_site.aniso_B[1][3]. XmlmmCIF equivalent: atom_site/aniso_B22 The [2][2] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. XmlmmCIF equivalent: atom_site/aniso_B22_esd The estimated standard deviation of _atom_site.aniso_B[2][2]. XmlmmCIF equivalent: atom_site/aniso_B23 The [2][3] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. XmlmmCIF equivalent: atom_site/aniso_B23_esd The estimated standard deviation of _atom_site.aniso_B[2][3]. XmlmmCIF equivalent: atom_site/aniso_B33 The [3][3] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. XmlmmCIF equivalent: atom_site/aniso_B33_esd The estimated standard deviation of _atom_site.aniso_B[3][3]. XmlmmCIF equivalent: atom_site/aniso_U11 The [1][1] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. XmlmmCIF equivalent: atom_site/aniso_U11_esd The estimated standard deviation of _atom_site.aniso_U[1][1]. XmlmmCIF equivalent: atom_site/aniso_U12 The [1][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. XmlmmCIF equivalent: atom_site/aniso_U12_esd The estimated standard deviation of _atom_site.aniso_U[1][2]. XmlmmCIF equivalent: atom_site/aniso_U13 The [1][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. XmlmmCIF equivalent: atom_site/aniso_U13_esd The estimated standard deviation of _atom_site.aniso_U[1][3]. XmlmmCIF equivalent: atom_site/aniso_U22 The [2][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. XmlmmCIF equivalent: atom_site/aniso_U22_esd The estimated standard deviation of _atom_site.aniso_U[2][2]. XmlmmCIF equivalent: atom_site/aniso_U23 The [2][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. XmlmmCIF equivalent: atom_site/aniso_U23_esd The estimated standard deviation of _atom_site.aniso_U[2][3]. XmlmmCIF equivalent: atom_site/aniso_U33 The [3][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. XmlmmCIF equivalent: atom_site/aniso_U33_esd The estimated standard deviation of _atom_site.aniso_U[3][3]. XmlmmCIF equivalent: atom_site/aniso_ratio Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. XmlmmCIF equivalent: atom_site/attached_hydrogens The number of hydrogen atoms attached to the atom at this site excluding any H atoms for which coordinates (measured or calculated) are given. XmlmmCIF equivalent: atom_site/auth_asym_id An alternative identifier for _atom_site.label_asym_id that may be provided by an author in order to match the identification used in the publication that describes the structure. XmlmmCIF equivalent: atom_site/auth_atom_id An alternative identifier for _atom_site.label_atom_id that may be provided by an author in order to match the identification used in the publication that describes the structure. XmlmmCIF equivalent: atom_site/auth_comp_id An alternative identifier for _atom_site.label_comp_id that may be provided by an author in order to match the identification used in the publication that describes the structure. XmlmmCIF equivalent: atom_site/auth_seq_id An alternative identifier for _atom_site.label_seq_id that may be provided by an author in order to match the identification used in the publication that describes the structure. Note that this is not necessarily a number, that the values do not have to be positive, and that the value does not have to correspond to the value of _atom_site.label_seq_id. The value of _atom_site.label_seq_id is required to be a sequential list of positive integers. The author may assign values to _atom_site.auth_seq_id in any desired way. For instance, the values may be used to relate this structure to a numbering scheme in a homologous structure, including sequence gaps or insertion codes. Alternatively, a scheme may be used for a truncated polymer that maintains the numbering scheme of the full length polymer. In all cases, the scheme used here must match the scheme used in the publication that describes the structure. XmlmmCIF equivalent: atom_site/calc_attached_atom The _atom_site.id of the atom site to which the 'geometry- calculated' atom site is attached. XmlmmCIF equivalent: atom_site/calc_flag A standard code to signal if the site data have been determined from the intensities or calculated from the geometry of surrounding sites, or have been assigned dummy coordinates. The abbreviation 'c' may be used in place of 'calc'. XmlmmCIF equivalent: atom_site/chemical_conn_number This data item is a pointer to _chemical_conn_atom.number in the CHEMICAL_CONN_ATOM category. XmlmmCIF equivalent: atom_site/constraints A description of the constraints applied to parameters at this site during refinement. See also _atom_site.refinement_flags and _refine.ls_number_constraints. XmlmmCIF equivalent: atom_site/details A description of special aspects of this site. See also _atom_site.refinement_flags. XmlmmCIF equivalent: atom_site/disorder_assembly A code which identifies a cluster of atoms that show long-range positional disorder but are locally ordered. Within each such cluster of atoms, _atom_site.disorder_group is used to identify the sites that are simultaneously occupied. This field is only needed if there is more than one cluster of disordered atoms showing independent local order. *** This data item would not in general be used in a macromolecular data block. *** XmlmmCIF equivalent: atom_site/disorder_group A code that identifies a group of positionally disordered atom sites that are locally simultaneously occupied. Atoms that are positionally disordered over two or more sites (e.g. the H atoms of a methyl group that exists in two orientations) can be assigned to two or more groups. Sites belonging to the same group are simultaneously occupied, but those belonging to different groups are not. A minus prefix (e.g. "-1") is used to indicate sites disordered about a special position. *** This data item would not in general be used in a macromolecular data block. *** XmlmmCIF equivalent: atom_site/footnote_id The value of _atom_site.footnote_id must match an id specified by _atom_sites_footnote.id in the ATOM_SITES_FOOTNOTE list. XmlmmCIF equivalent: atom_site/fract_x The x coordinate of the atom site position specified as a fraction of _cell.length_a. XmlmmCIF equivalent: atom_site/fract_x_esd The estimated standard deviation of _atom_site.fract_x. XmlmmCIF equivalent: atom_site/fract_y The y coordinate of the atom site position specified as a fraction of _cell.length_b. XmlmmCIF equivalent: atom_site/fract_y_esd The estimated standard deviation of _atom_site.fract_y. XmlmmCIF equivalent: atom_site/fract_z The z coordinate of the atom site position specified as a fraction of _cell.length_c. XmlmmCIF equivalent: atom_site/fract_z_esd The estimated standard deviation of _atom_site.fract_z. XmlmmCIF equivalent: atom_site/group_PDB The group of atoms to which the atom site belongs. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. XmlmmCIF equivalent: atom_site/label_alt_id A component of the macromolecular identifier for this atom site. For further details, see the definition of the ATOM_SITE_ALT category. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. XmlmmCIF equivalent: atom_site/label_asym_id A component of the macromolecular identifier for this atom site. For further details, see the definition of the STRUCT_ASYM category. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. XmlmmCIF equivalent: atom_site/label_atom_id A component of the macromolecular identifier for this atom site. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. XmlmmCIF equivalent: atom_site/label_comp_id A component of the macromolecular identifier for this atom site. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. XmlmmCIF equivalent: atom_site/label_entity_id This data item is a pointer to _entity.id in the ENTITY category. XmlmmCIF equivalent: atom_site/label_seq_id This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. XmlmmCIF equivalent: atom_site/occupancy The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. XmlmmCIF equivalent: atom_site/occupancy_esd The estimated standard deviation of _atom_site.occupancy. XmlmmCIF equivalent: atom_site/pdbx_PDB_atom_name PDB atom name. XmlmmCIF equivalent: atom_site/pdbx_PDB_ins_code PDB insertion code. XmlmmCIF equivalent: atom_site/pdbx_PDB_model_num PDB model number. XmlmmCIF equivalent: atom_site/pdbx_PDB_residue_name PDB residue name. XmlmmCIF equivalent: atom_site/pdbx_PDB_residue_no PDB residue number. XmlmmCIF equivalent: atom_site/pdbx_PDB_strand_id PDB strand id. XmlmmCIF equivalent: atom_site/pdbx_auth_alt_id Author's alternate location identifier. XmlmmCIF equivalent: atom_site/pdbx_auth_atom_name Author's atom name. XmlmmCIF equivalent: atom_site/refinement_flags A concatenated series of single-letter codes which indicate the refinement restraints or constraints applied to this site. XmlmmCIF equivalent: atom_site/restraints A description of restraints applied to specific parameters at this site during refinement. See also _atom_site.refinement_flags and _refine.ls_number_restraints. XmlmmCIF equivalent: atom_site/symmetry_multiplicity The multiplicity of a site due to the space-group symmetry as is given in International Tables for Crystallography, Vol. A (1987). XmlmmCIF equivalent: atom_site/thermal_displace_type A standard code used to describe the type of atomic displacement parameters used for the site. XmlmmCIF equivalent: atom_site/type_symbol This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. XmlmmCIF equivalent: atom_site/id The value of _atom_site.id must uniquely identify a record in the ATOM_SITE list. Note that this item need not be a number; it can be any unique identifier. This data item was introduced to facilitate compatibility between small molecule and macromolecular files. In the small molecule files, _atom_site_label is the identifier for the atom. In the macromolecular files, the atom identifier is the aggregate of _atom_site.label_alt_id, _atom_site.label_asym_id, _atom_site.label_atom_id, _atom_site.label_comp_id and _atom_site.label_seq_id. For the two types of files to be compatible, a formal identifier for the category had to be introduced that was independent of the different modes of identifying atoms. For compatibility with older files, _atom_site_label is aliased to _atom_site.id.