menucheckCIF procedure
PROC-NAME: CHEMW03 Type_2PURPOSE: To check that the _chemical_formula_weight matches that calculated for the atomic content data from the two lists, _atom_site_ and _atom_type_, using the number of formula units per cell and the number of symmetry equivalent positions {NSYM from procedure SM}.
PROCEDURE:
SUMMATION
(1) Match the element symbol with the _atom_site_label in the _atom_site_ list and sum the atomic weights for all sites, multiplying by the _atom_site_occupancy value and the symmetry site-multiplicity value (generated from NSYM).
(2) Additionally, if the _atom_type_ list is present in the CIF, sum the atomic weights for the _atom_type_number_in_cell for each element.
CALCULATE
XX = SUM of (1)[or (2)] / _cell_formula_units_Z
WT = XX * NSYM
RC = _chemical_formula_weight / WT
TEST
IF RC
0.90 <> 1.10 issue ALERT Level A (> 10% difference)
"ALERT: The ratio of given/expected molecular weight as calculated from the _atom_site*(or type) data lies outside the range 0.90 <> 1.10"
0.95 <> 1.05 issue ALERT Level B (> 5% difference)
"WARNING: The ratio of given/expected molecular weight as calculated from the _atom_site*(or type) data lies outside the range 0.95 <> 1.05 "
0.99 <> 1.01 issue ALERT Level C (> 1% difference)
"The ratio of given/expected molecular weight as calculated from the _atom_site*(or type) data lies outside the range 0.99 <> 1.01"
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The formula weight given in the CIF differs from that calculated using
the _atom_site_ list (i.e. the list of atomic coordinates). Check that
you have calculated the formula weight correctly and that it corresponds
with the true sum of all elements in all distinct moieties present,
including any solvent and all H atoms. This message can be ignored if
the model is intentionally incomplete 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 _chemical_formula_weight. 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. Similarly, this alert could appear if you have given the following loop structure:
loop_ A discrepancy between the formula weight derived from this list and the formula weight given under _chemical_formula_weight may mean that the atom counts in the loop are incorrect or that _chemical_formula_weight has been incorrectly specified. Once again, _atom_type_symbol and _atom_type_number_in_cell must correspond with the true contents of the unit cell, including any solvent and all H atoms. |
