menucheckCIF procedure
PROC-NAME: FORMU01 Type_1/2PURPOSE: To check that the total sum formulae derived from the _chemical_formula_sum _chemical_formula_moiety, _atom_site_ and _atom_type_ data all match.
PROCEDURE:
CALCULATE
(1). Sum formula derived from the _chemical_formula_moiety using the rules in the CIF-dictionary. Type_1
(2). Sum formula from the _atom_site_ items taking into account the _atom_site_occupancy and symmetry as appropriate. Type_1
(3). Sum formula from the _atom_type_ items (if present). Type_2
TEST
IF the atom count is > 0.01 atom, from that given by the _chemical_formula_sum
THEN issue a General ALERT
For (1)
"There is a discrepancy between the atom counts in the _chemical_formula_sum and _chemical_formula_moiety. This is usually due to the moiety formula being in the wrong format."
|
_chemical_formula_moiety has the identical format to _chemical_formula_sum,
namely C, H, then alphabetical, with the exception that the individual
unconnected independent entities in the structure are listed separately.
A common mistake is to attempt to depict organometallic coordination with
this entry. Such coordination can be given under
_chemical_formula_structural or _chemical_formula_IUPAC if desired, but
must never be given as _chemical_formula_moiety. Furthermore, do not
use subscript formatting: C10 H20 is correct, C~10~ H~20~ is not. Nesting
of parentheses is also not allowed.
Correct examples:
Formulae like '[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H' and
'(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2' are INCORRECT for
_chemical_formula_moiety. If _chemical_formula_moiety has been given in the correct style, then there is a discrepancy between the atom counts in one or more of the moieties and the total calculated over all moieties. Check that there is not a typographical error in _chemical_formula_moiety and _chemical_formula_sum and that the actual moieties present in the structure have been interpreted correctly. Both _chemical_formula_moiety and _chemical_formula_sum must correspond with the true species present, including any solvent, and not the contents implied by the model if there are differences due to the omission of a few H atoms or solvent atoms. If multiple moieties such as solvent are present, or one of the moieties possesses or is disordered about a crystallographic symmetry element, ensure that the correct ratio of moieties has been allowed for in the calculation of Z, _chemical_formula_moiety and _chemical_formula_sum. |
"There is a discrepancy between the atom counts in the _chemical_formula_sum and the formula from the _atom_type* data."
|
There is a discrepancy between the total number of each element
in the unit cell calculated from Z * _chemical_formula_sum and
that given in the loop structure: loop_ _atom_type_symbol _atom_type_description _atom_type_number_in_cell Check that the entries under _cell_formula_units_Z, _chemical_formula_sum and in the above loop are given correctly and completely. _chemical_formula_sum must correspond with the true sum of all elements in all distinct moieties present, including any solvent and all H atoms, and not the contents implied by the model if there are differences due to the omission of a few H atoms or solvent atoms. Similarly, the atom_type_* loop must indicate the total number of each element type expected to be present in the entire unit cell, including all solvent and H atoms. If multiple moieties such as solvent are present, or one of the moieties possesses or is disordered about a crystallographic symmetry element, ensure that the correct ratio of moieties has been allowed for in the calculation of Z and _chemical_formula_sum. _chemical_formula_sum must also be in the correct format (e.g. do not use subscript formatting: C10 H20 is correct, C~10~ H~20~ is not). |
"There is a discrepancy between the atom counts in the _chemical_formula_sum and the formula from the _atom_site* data."
|
There is a difference between the atom count derived from
_chemical_formula_sum and from the _atom_site_ list (i.e
the list of atomic coordinates). Check that _chemical_formula_sum
is given correctly and in the correct format (e.g. do not use
subscript formatting: C10 H20 is correct, C~10~ H~20~ is not).
Of course, _chemical_formula_sum must correspond with the true sum of all elements in all distinct moieties present, including any solvent and all H atoms, and not the contents implied by the model if there are differences due to the omission of a few H atoms or solvent atoms. In this case, this message can be ignored. However, be sure that the model is indeed otherwise complete and that no elements have been misassigned. If multiple moieties such as solvent are present, or one of the moieties possesses or is disordered about a crystallographic symmetry element, ensure that the correct ratio of moieties has been allowed for in the calculation of Z and _chemical_formula_sum. However, this alert could also be an indication of overlooked errors in the model. Be sure that the model is indeed as complete as intended and that no elements have been misassigned. Also check that the atom site occupancy is correct for the atomic coordinates otherwise a mismatch may be encountered [e.g an atom on a 2-fold axis normally has a site occupancy of 1.0 (but a multiplicity of 0.5)]. Furthermore, the site occupancy for disordered atomic sites should always sum to 1.0 when all of the alternative disordered sites are considered. |
