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：使用每個(gè)單胞中的分子式單位和對(duì)稱(chēng)等效位置(NSYM來(lái)自SM過(guò)程)來(lái)檢查_(kāi)chemical_formula_weight是否與從_atom_site_和_atom_type_兩個(gè)列表計(jì)算的原子含量數(shù)據(jù)相匹配。

過(guò)程：

求和

(1)將元素符號(hào)與_atom_site_列表中的_atom_site_label匹配，并對(duì)所有占位的原子量求和，然后乘以_atom_site_occupancy值和對(duì)稱(chēng)占位多重性值(由NSYM產(chǎn)生)。(2)另外，若CIF中存在_atom_type_列表，則對(duì)每個(gè)元素的_atom_type_number_in_cell原子量求和。

計(jì)算

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

WT = XX * NSYM

RC = _chemical_formula_weight / WT

檢查

若 RC

小于0.90或大于1.10，則發(fā)布A級(jí)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，則發(fā)布B級(jí)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，則發(fā)布C級(jí)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中給出的分子量與使用_atom_site_列表(即原子坐標(biāo)列表)計(jì)算出的分子量不同。檢查是否已正確計(jì)算分子量，并且該分子量與存在的所有不同部分(包括任何溶劑和所有氫原子)中所有元素的真實(shí)綜合相對(duì)應(yīng)。如果是由于故意刪除一些氫原子或溶劑原子而使模型不完整，則可以忽略此消息。

? ? ? ??若存在多個(gè)部分(如溶劑)，或其中一個(gè)部分具有或關(guān)于晶體學(xué)對(duì)稱(chēng)元素的無(wú)序，則請(qǐng)確保在計(jì)算_chemical_formula_weight時(shí)已考慮到正確的部分比例。

? ? ? ? 但是，此警告也可能暗示模型中存在被忽視的錯(cuò)誤。請(qǐng)確保模型確實(shí)如預(yù)期的那樣完整并且沒(méi)有元素指認(rèn)錯(cuò)誤。

? ? ? ? 另外，請(qǐng)檢查原子坐標(biāo)的原子位置占有率是否正確，否則可能會(huì)發(fā)生不匹配[例如，處于二重軸上的位置通常位置占有率為1.0(但多重度為0.5)]。此外，當(dāng)考慮所有其他無(wú)序位置時(shí)，無(wú)序原子位置的位置占有率之和始終為1.0。

? ? ? ? 同樣，若給出如下循環(huán)結(jié)構(gòu)，則此警告也可能會(huì)出現(xiàn)：

? ? ? ? loop_

? ? ? ? ? _atom_type_symbol

? ? ? ? ? _atom_type_description

? ? ? ? ? _atom_type_number_in_cell

? ? ? ? 從該表得出的分子量與_chemical_formula_weight給出的分子量之間的差異可能表示循環(huán)中的原子數(shù)目不正確，或者_(dá)chemical_formula_weight指定不正確。再次強(qiáng)調(diào)，_atom_type_symbol和_atom_type_number_in_cell必須與單胞中的真實(shí)內(nèi)容相對(duì)應(yīng)，包括任何溶劑和所有氫原子。

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值沒(méi)有給對(duì)。

解決策略：在ins里給對(duì)分子式和Z值重新精修生成CIF。若使用Olex2軟件，則可填好Z'后精修重新生成CIF即可。