cif_cod.dic

Version: 0.036 (2018-10-08)

  1. COD_DUPLICATE
    1. _cod_duplicate_entry
  2. COD_DATA_SOURCE
    1. _cod_data_source_file
    2. _cod_data_source_URI
    3. _cod_data_source_URL
    4. _cod_data_source_URN
    5. _cod_data_source_block
    6. _cod_data_source_MD5_sum
    7. _cod_data_source_SHA1_sum
    8. _cod_data_source_SHA256_sum
  3. COD_ERROR
    1. _cod_error_flag
    2. _cod_error_source
    3. _cod_error_description
  4. COD_DATABASE
    1. _cod_database_code
    2. _cod_database_fobs_code
    3. _cod_database_coordinates_code
  5. COD_DEPOSITOR
    1. _cod_depositor_comments
  6. COD_RELATED
    1. _cod_related_optimal_struct
    2. _cod_related_suboptimal_struct
  7. COD_RELATED_ENTRY
    1. _cod_related_entry_id
    2. _cod_related_entry
    3. _cod_related_entry_code
    4. _cod_related_entry_database
    5. _cod_related_entry_description
    6. _cod_related_entry_uri
  8. COD_ORIGINAL
    1. _cod_original_cell_volume
    2. _cod_original_formula_weight
    3. _cod_original_formula_units_Z
    4. _cod_original_formula_sum
    5. _cod_original_formula_moiety
    6. _cod_original_formula_iupac
    7. _cod_original_sg_symbol_H-M
    8. _cod_original_sg_symbol_Hall
    9. _cod_original_sg_number
    10. _cod_chemical_formula_sum_orig
    11. _cod_chemical_formula_moiety_orig
    12. _cod_cif_authors_sg_H-M
    13. _cod_cif_authors_sg_Hall
    14. _cod_cif_authors_sg_number
  9. COD_MOLECULE_ATOM
    1. _cod_molecule_atom_label
    2. _cod_molecule_atom_orig_label
    3. _cod_molecule_atom_symmetry
    4. _cod_molecule_atom_symop_id
    5. _cod_molecule_atom_symop_xyz
    6. _cod_molecule_atom_transl_id
    7. _cod_molecule_atom_transl_x
    8. _cod_molecule_atom_transl_y
    9. _cod_molecule_atom_transl_z
    10. _cod_molecule_atom_mult
    11. _cod_molecule_atom_mult_ratio
    12. _cod_molecule_atom_assembly
    13. _cod_molecule_atom_group
  10. COD_MOLECULE_TRANSFORM
    1. _cod_molecule_transform_label
    2. _cod_molecule_transform_symop

COD_DUPLICATE

Data items in this category are to be used for flagging and managing duplicate entries when they are spotted in the COD.

_cod_duplicate_entry

Specifies that the COD entry containing this data item is considered to be a duplicate of another entry. The COD ID of this other entry, which is considered to be "primary" entry for the structure, is specified as a value of this data item. As a rule, the "primary" entry should be the most complete and comprehensive structure description in the COD.

This data item is intended to give hints as to which entries carry exactly the same information and might be excluded from statistics. Normally, the duplicates are not deposited into the COD; if a duplicate is already in the COD collection, however, it cannot be simply removed since COD IDs are assigned permanently. Thus, this data item is used to flag such entries when noticed.

COD_DATA_SOURCE

Data items from this category are used to record and trace sources of information deposited into the COD.

_cod_data_source_file

Specifies the name of the file that served as the source of the data for this COD entry. The file name should be recoded without the path or other URL components since these components usually have no sense on the recipient's system. In Unix parlance, the value recorded should be the basename of the original file. If the full, permanent URL or URN is known and recorded the _cod_data_source_URN or _cod_data_source_URL data items should be used instead.

For many data sources, however, the basename contains enough information to locate the original source. For instance, CIFs published in IUCr journals have a Coeditor Code as a CIF file name permitting to identify the original paper where the structure is discussed. Other journals may use the DOI of the original article as a part of the file name of the supplementary CIF file, which also permits one to trace back the original paper.

_cod_data_source_URI

Specifies the uniform resource identifier (URI) of the file that served as a source of data in this COD entry. If the full, permanent URI is known and recorded, this may be used instead of _cod_data_source_file. For many data sources, however, the basename contains enough information to locate the original source. See full discussion under _cod_data_source_file.

_cod_data_source_URL

Specifies the uniform resource locator (URL) of the file that served as a source of data in this COD entry. If the full, permanent URL is known and recorded, this may be used instead of _cod_data_source_file. For many data sources, however, the basename contains enough information to locate the original source. See full discussion under _cod_data_source_file.

_cod_data_source_URN

Specifies the uniform resource name (URN) of the file that served as a source of data in this COD entry. If the full, permanent URN is known and recorded, this may be used instead of _cod_data_source_file. For many data sources, however, the basename contains enough information to locate the original source. See full discussion under _cod_data_source_file.

_cod_data_source_block

Specifies the name of the data block within the file specified using the _cod_data_source_file data item that served as a source of data in this COD entry. Only the data block name following the 'data_' header keyword should be recorded, not the whole data block header; i.e. the value specified here should be 'I', *not* 'data_I', for a data block with the header 'data_I'.

Currently, only one source of data, the data block that contained cell constants and atomic coordinates, is recorded, and thus this data item is not placed into a loop. If the data source file is not a CIF, this data iten is irrelevant and may be omitted or may contain value '.' (dot).

_cod_data_source_MD5_sum

Provides MD5 cryptographic checksum of the source data file that was used to generate this COD entry. The checksum should be computed from the same file that is referenced using the _cod_data_source_file data item.

_cod_data_source_SHA1_sum

Provides SHA1 cryptographic checksum of the source data file that was used to generate this COD entry. The checksum should be computed from the same file that is referenced using the _cod_data_source_file data item.

_cod_data_source_SHA256_sum

Provides SHA256 cryptographic checksum of the source data file that was used to generate this COD entry. The checksum should be computed from the same file that is referenced using the _cod_data_source_file data item.

COD_ERROR

Data from this category flag and describe problems (errors, warnings, etc.) that were discovered in a particular COD entry during deposition, validation or review.

_cod_error_flag

Describes the severity of errors if such are detected in COD entries:

'none': means that the entry is clean and can be used with confidence; normally the data item with this value can be omitted.

'warnings': data or syntax have suspicious properties, or some missing pieces of information, but the main data items (unit cell, coordinates, chemical formula) should be mostly correct.

           Warnings may be used to indicate internal
           inconsistencies (e.g. mismatches between declared
           chemical formula sum and the actual atomic composition)
           that do not show an obviously incorrect structure;
           unusual bond geometries, valencies, packing voids, etc.

'errors': the file has serious errors; the data are either wrong or unusable due to dictionary non-conformance, obvious data errors, known experimental errors, missing data items.

'retracted': the original paper describing the structure, or the COD CIF file was retracted by authors.

Values:

ValueDescription
noneno errors are detected in this entry (may be omitted)
warningssome suspicious properties of the data or syntax
errorsmistakes in the file that make data unusable
retractedstructure or paper was retracted by authors

_cod_error_source

Describes the most distant (i.e. the closest to the data origin) COD source where the origin of the detected problem (error, warning, etc.) can be traced back.

Values:

ValueDescription
depositionProblems were introduced at the stage of structure deposition to COD. The entry should be corrected after consulting the original data source if it is available.
upstreamProblems were introduced in the intermediate source (another database, Web site, review publication, etc.) from which COD obtained data, but the original publication is either not found or is correct. In the latter case, obviously, the problem will be corrected from the original publication, but the erroneous COD entry can be flagged for documentation purposes and committed to the version control repository before correction.
originalProblem can be traced back to the original publication. Despite the problem in the publication, there are no indications however that the experiment was performed incorrectly.
experimentProblems were introduced when performing the experiment.
unknownThe source of the problem is not known.

_cod_error_description

Provides a human-readable description of the problems identified in the COD entry bearing the _cod_error_* records.

COD_DATABASE

Data items from this category are used for COD bookkeeping records, such as the assigned COD ID (a.k.a COD database code).

_cod_database_code

Specifies the COD ID assigned upon deposition into COD to the crystal structure described in the CIF.

_cod_database_fobs_code

Specifies the COD ID of the Fobs file. Normally, the same ID is assigned in the COD for both the coordinates and the structure factor (a.k.a Fobs) CIF; for powder diffraction experiments, however, one set of diffractograms will be assigned a single COD ID, and all phases refined against them will refer to this single observed data COD ID, while each phase will get a distinct COD ID of its own. It may be usual, although not required, that the diffractogram set gets the same COD ID as is assigned to the first phase in the experiment.

_cod_database_coordinates_code

Specifies COD ID(s) of coordinate files that were determined from this observed dataset; to be inserted into COD Fobs (.hkl) files.

COD_DEPOSITOR

Data items from this category are used for adding COD depositor comments, notes, structure rating, remarks.

_cod_depositor_comments

Human readable comments from COD depositors, and human readable log records from CIF processing programs.

COD_RELATED

Data items in this category describe related entries in COD or other databases. Related entries may contain alternative results on the same structure, structures of the same compound under different conditions, theoretical models of the same compound (if such are published in the same paper as the experimental structure for comparison), or examples of alternative structure interpretation (using different space group or setting).

Some of these related structures might be suboptimal, i.e. they may contain interpretation of the structural data that was deliberately processed in a way that is not the best and are provided here only for reference and comparison purposes. Care should be taken that such suboptimal structures are not used for computations or statistics, except when comparing with the related optimal structure.

_cod_related_optimal_struct

Contains a COD database code for the COD entry that contains the optimally solved structure for the crystal or compound under consideration. This optimal structure should be used for all inferences; the current suboptimal structure is provided for illustration purposes only (e.g. to demonstrate that an alternative space group choice, structure solution method, or assumptions are indeed inferior and thus the optimal structure contains the correct ones).

_cod_related_suboptimal_struct

Contains COD database code or codes for suboptimal solutions of the same structure that may be provided by authors in the discussion of their structure solution strategy to provide evidence that the current structure is indeed solved correctly and in the best possible way.

COD_RELATED_ENTRY

The CATEGORY of data items used to describe the relationship between a COD entry and related entries in the COD or other databases. Related entries may contain alternative results on the same structure, structures of the same compound under different conditions, theoretical models of the same compound (if such are published in the same paper as the experimental structure for comparison), or examples of alternative structure interpretation (using different space group or setting).

_cod_related_entry_id

Value is a unique key to a set of COD_RELATED_ENTRY items in a looped list.

_cod_related_entry

Contains database codes (COD, PCOD or TCOD IDs, PDB identifiers, etc.) for structures that are in some way related to the current structure (e.g. the same compound solved under different conditions, etc.)

_cod_related_entry_code

Contains database codes (COD, PCOD or TCOD IDs, PDB identifiers, etc.) for structures that are in some way related to the current structure (e.g. the same compound solved under different conditions, etc.)

_cod_related_entry_database

Contains the name of a database in which the related entry (with the code given in _cod_related_entry_code) is stored. If this data value is not given or has the value '.', it should be assumed that the code given in _cod_related_entry_code refers to the same database as the entry which is under discussion (i.e. from which the _cod_related_entry_code code is taken).

_cod_related_entry_description

A human-readable short description of the related entry ‒ how it is related to the current entry.

_cod_related_entry_uri

The uniform resource identifier (URI) of the related entry given in the _cod_related_entry_code data item.

COD_ORIGINAL

Data items in this category record the original (author-supplied) values of certain data items subsequently altered in accordance with values computed by the COD scripts.

_cod_original_cell_volume

Original crystal unit cell volume provided by CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored in the regular '_cell_volume' data item value).

_cod_original_formula_weight

Original chemical formula mass in daltons provided by CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored in the regular '_chemical_formula_weight' data item value).

_cod_original_formula_units_Z

Original number of the formula units in the unit cell provided by CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored in the regular '_cell_formula_units_Z' data item value).

_cod_original_formula_sum

Original chemical formula in which all discrete bonded residues and ions are summed over the constituent elements following the Hill system ordering provided by CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored in the regular '_chemical_formula_sum' data item value).

_cod_original_formula_moiety

Original chemical formula with each discrete bonded residue or ion shown as a separate moiety provided by CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored in the regular '_chemical_formula_moiety' data item value).

_cod_original_formula_iupac

Original chemical formula expressed in conformance with IUPAC rules for inorganic and metal-organic compounds where these conflict with the rules for any other _chemical_formula_ entries provided by the CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored in the regular '_chemical_formula_iupac' data item value).

_cod_original_sg_symbol_H-M

Original Hermann-Mauguin space group symbol provided by CIF authors. Should be provided if it is different from the value computed by COD scripts (stored in the regular '_symmetry_space_group_name_H-M' data item value).

_cod_original_sg_symbol_Hall

Original space group symbol as described by Hall provided by CIF authors. Should be provided if it is different from the value computed by COD scripts (stored in the regular '_symmetry_space_group_name_Hall' data item value).

_cod_original_sg_number

Original space group number from International Tables for Crystallography Vol. A (2002) provided by CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored in the regular '_space_group_IT_number' data item value).

_cod_chemical_formula_sum_orig

Original chemical formula in which all discrete bonded residues and ions are summed over the constituent elements following the Hill system ordering provided by CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored in the regular '_chemical_formula_sum' data item value).

_cod_chemical_formula_moiety_orig

Original chemical formula with each discrete bonded residue or ion shown as a separate moiety. Should be provided if it is different from the value computed by the COD scripts (stored in the regular '_chemical_formula_moiety' data item value).

_cod_cif_authors_sg_H-M

Original Hermann-Mauguin space group symbol provided by CIF authors. Should be provided if it is different from the value computed by COD scripts (stored in the regular '_symmetry_space_group_name_H-M' date item value).

_cod_cif_authors_sg_Hall

Original space group symbol as described by Hall provided by CIF authors. Should be provided if it is different from the value computed by COD scripts (stored in the regular '_symmetry_space_group_name_Hall' data item value).

_cod_cif_authors_sg_number

Original space group number from International Tables for Crystallography Vol. A (2002) provided by CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored in the regular '_space_group_IT_number' data item value).

COD_MOLECULE_ATOM

Data items from this category are used to describe details of atoms of restored molecules. Data items belonging to this category are written by the cif_molecule script from svn://www.crystallography.net/cod-tools repository. Data items belonging to this category are read by the cif_bonds_angles and some other scripts from svn://saulius-grazulis.lt/atomclasses repository.

_cod_molecule_atom_label

Label of an atom, restored from asymmetric unit using symmetry operators.

_cod_molecule_atom_orig_label

Label denoting the original atom, from which symmetrically equivalent atom was restored.

_cod_molecule_atom_symmetry

Description of transformation applied to the original atom, producing the symmetry equivalent, in the form S_ABC, where S is the number of the symmetry operator, given in the _symmetry_equiv_pos_as_xyz list, and A-5, B-5 and C-5 denote the translation along the x, y and z axes respectively.

_cod_molecule_atom_symop_id

Number of the symmetry operator from the _symmetry_equiv_pos_as_xyz list, that was used to produce the symmetry equivalent of the original atom.

_cod_molecule_atom_symop_xyz

Symmetry operator, that was used to produce the symmetry equivalent of the original atom.

_cod_molecule_atom_transl_id

Translation identifier in the form of 'ABC', where A-5, B-5 and C-5 denotes translation along x, y and z axes respectively.

_cod_molecule_atom_transl_x

Translation along the x axis.

_cod_molecule_atom_transl_y

Translation along the y axis.

_cod_molecule_atom_transl_z

Translation along the z axis.

_cod_molecule_atom_mult

Number of total crystal symmetry operators divided by site's multiplicity ratio, as given in _cod_molecule_atom_mult_ratio.

_cod_molecule_atom_mult_ratio

Multiplicity ratio: number of crystal symmetry operators that map this atom site to itself.

_cod_molecule_atom_assembly

A code which identifies a cluster of atoms in the restored molecule that show long-range positional disorder but are locally ordered. Within each such cluster of atoms, _cod_molecule_atom_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.

_cod_molecule_atom_group

A code which 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 hydrogen 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.

COD_MOLECULE_TRANSFORM

Data items from this category are used to list symmetry operators mapping an original atom to each of its symmetry equivalents. Data items belonging to this category are written by the cif_molecule script from svn://www.crystallography.net/cod-tools repository. Data items belonging to this category are read by the cif_bonds_angles and some other scripts from svn://saulius-grazulis.lt/atomclasses repository.

_cod_molecule_transform_label

Label of an atom restored from the asymmetric unit using symmetry operators.

_cod_molecule_transform_symop

Symmetry operator that maps the original atom to its symmetry equivalent.