menucheckCIF procedure
PROC-NAME: CELLZ01 Type_1PURPOSE: To check that the cell contents calculated from _chemical_formula_sum and _cell_formula_units_Z matches that from the atom sites present in the _atom_site_ list and the _symmetry_ information.
PROCEDURE:
SUMMATION
(1) For each atomic species in the _chemical_formula_sum string, calculate the number of atoms in the cell using the _chemical_formula_sum counts and the _cell_formula_units_Z.
(2) For each atomic species in the _atom_site_ list, calculate, using the _atom_site_occupancy value and the symmetry site-multiplicity value (generated from NSYM), the number of atoms in the cell.
CALCULATE
DN = [cell contents from (1)] - [cell contents from (2)] for each atom type
SUMDN = sum of DN for ALL atom species
TEST
IF atom counts in (1) differ from those declared in the _atom_type_
list (if present) issue General ALERT
"WARNING: Cell contents from the formula and atom_type data differ!"
|
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. 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). |
"Input H-M symbol mismatch with Hall symbol"
|
Check that the entries given under _symmetry_space_group_name_H-M
and _symmetry_space_group_name_Hall refer to the same space group
and setting and do not have typographical errors. Note that space
group symbols under _symmetry_space_group_name_H-M should not
have typesetting formatting included (e.g. subscripts).
Example:
Also interpreted correctly by CHECKCIF is:
Incorrect are: |
IF SUMDN > 0.05 issue the General ALERT
"Difference between formula and atom_site contents detected."
AND THEN
IF SUMDN < 0.5 issue the General ALERT
"ALERT: Check formula stoichiometry or atom site occupancies."
|
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. _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). 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. |
IF DN for Hydrogen atoms > 0.5 issue the General ALERT
"WARNING: H atoms missing from atom site list. Is this intentional?"
| H atoms must be included in the model as far as possible. Exceptions might be where the H atoms cannot be located and their positions cannot otherwise be calculated or predicted from geometrical considerations. For example, with solvent or coordinated water H atoms or in severely disordered groups or solvent molecules. |
ELSE issue the General ALERT
"ALERT: Large difference may be due to symmetry error - see SYMMG tests."
