CheckCIF-CHEMW03

PROC-NAME: CHEMW03 Type_2

PURPOSE: 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"

        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_

          _atom_type_symbol

          _atom_type_description

          _atom_type_number_in_cell

        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.

(http://journals.iucr.org/services/cif/checking/CHEMW_03.html)

目的：使用每个单胞中的分子式单位和对称等效位置(NSYM来自SM过程)来检查_chemical_formula_weight是否与从_atom_site_和_atom_type_两个列表计算的原子含量数据相匹配。

过程：

求和

(1)将元素符号与_atom_site_列表中的_atom_site_label匹配，并对所有占位的原子量求和，然后乘以_atom_site_occupancy值和对称占位多重性值(由NSYM产生)。(2)另外，若CIF中存在_atom_type_列表，则对每个元素的_atom_type_number_in_cell原子量求和。

计算

XX = SUM of (1)[or (2)] / _cell_formula_units_Z

WT = XX * NSYM

RC = _chemical_formula_weight / WT

检查

若 RC

小于0.90或大于1.10，则发布A级警告(差值大于10%)

         "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"

小于0.95或大于1.05，则发布B级警告(差值大于5%)

         "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 "

小于0.99或大于1.01，则发布C级警告(差值大于1%)

         "The ratio of given/expected molecular weight as calculated from the _atom_site*(or type) data lies outside the range 0.99 < > 1.01"

        CIF中给出的分子量与使用_atom_site_列表(即原子坐标列表)计算出的分子量不同。检查是否已正确计算分子量，并且该分子量与存在的所有不同部分(包括任何溶剂和所有氢原子)中所有元素的真实综合相对应。如果是由于故意删除一些氢原子或溶剂原子而使模型不完整，则可以忽略此消息。

        若存在多个部分(如溶剂)，或其中一个部分具有或关于晶体学对称元素的无序，则请确保在计算_chemical_formula_weight时已考虑到正确的部分比例。

        但是，此警告也可能暗示模型中存在被忽视的错误。请确保模型确实如预期的那样完整并且没有元素指认错误。

        另外，请检查原子坐标的原子位置占有率是否正确，否则可能会发生不匹配[例如，处于二重轴上的位置通常位置占有率为1.0(但多重度为0.5)]。此外，当考虑所有其他无序位置时，无序原子位置的位置占有率之和始终为1.0。

        同样，若给出如下循环结构，则此警告也可能会出现：

        loop_

          _atom_type_symbol

          _atom_type_description

          _atom_type_number_in_cell

        从该表得出的分子量与_chemical_formula_weight给出的分子量之间的差异可能表示循环中的原子数目不正确，或者_chemical_formula_weight指定不正确。再次强调，_atom_type_symbol和_atom_type_number_in_cell必须与单胞中的真实内容相对应，包括任何溶剂和所有氢原子。

例：CHEMW03_ALERT_2_A ALERT: The ratio of given/expected molecular weight as calculated from the _atom_site* data lies outside the range 0.90 <> 1.10

From the CIF: _cell_formula_units_Z 4

From the CIF: _chemical_formula_weight 115.43

TEST: Calculate formula weight from _atom_site_*

        atom     mass    num     sum

        C       12.01    8.50    102.09

        H       1.01     9.50    9.58

        N       14.01    2.50    35.02

        O       16.00    2.50    40.00

        Cu      63.55    0.50    31.77

        Cl       35.45    0.50    17.73

Calculated formula weight   236.18

警告原因：分子式和Z值没有给对。

解决策略：在ins里给对分子式和Z值重新精修生成CIF。若使用Olex2软件，则可填好Z'后精修重新生成CIF即可。