PROC-NAME: FORMU01 Type_1/2

PURPOSE: 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:

? ? ? ? _chemical_formula_moiety?? 'C7 H4 Cl Hg N O3 S'

? ? ? ? _chemical_formula_moiety?? 'C12 H17 N4 O S 1+, C6 H2 N3 O7 1-'

? ? ? ? _chemical_formula_moiety?? 'C12 H16 N2 O6, 5(H2 O1)'

? ? ? ? _chemical_formula_moiety?? '(Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O)'

? ? ? ? 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.

? ? ? ? However these can be given as:

? ? ? ? _chemical_formula_IUPAC???? '[Co Re (C12 H22 P)2 (C O)6].0.5(C H3 O H)'

? ? ? ? _chemical_formula_structural?? '(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2'

? ? ? ? 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.

For (2)

? ? ? ??? "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).

For (3)

? ? ? ?? "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.

(http://journals.iucr.org/services/cif/checking/FORMU_01.html)

目的：檢查從_chemical_formula_sum、_chemical_formula_moiety、_atom_site_和_atom_type_產(chǎn)生的總和分子式數(shù)據(jù)是否都匹配。

過(guò)程：

計(jì)算

(1). 使用CIF詞典中的規(guī)則從_chemical_formula_moiety導(dǎo)出的總分子式。 Type_1

(2). 正確考慮_atom_site_occupancy和對(duì)稱性從_atom_site_條目計(jì)算得到的總分子式。Type_1

(3). 來(lái)自_atom_type_條目(若存在)的總分子式。Type_2

檢查TEST

若原子數(shù)大于_chemical_formula_sum 給出的原子數(shù)的0.01倍

則發(fā)布一般警告

對(duì)于(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具有與_chemical_formula_sum相同的格式，即按照C，H，然后按字母順序排序的格式，但結(jié)構(gòu)中各個(gè)未連接的獨(dú)立實(shí)體分開(kāi)列出。一個(gè)常見(jiàn)的錯(cuò)誤是試圖用該條目來(lái)描述金屬有機(jī)配位。如有需要，這樣的配位可以在_chemical_formula_structural或_chemical_formula_IUPAC條目中給出，但絕不能在_chemical_formula_moiety條目中給出。此外，請(qǐng)勿使用下標(biāo)格式：C10 H20為正確格式，C~10~ H~20~為錯(cuò)誤格式。也不允許嵌套括號(hào)。

? ? ? ? 正確示例：

? ? ? ? _chemical_formula_moiety?? 'C7 H4 Cl Hg N O3 S'

? ? ? ? _chemical_formula_moiety?? 'C12 H17 N4 O S 1+, C6 H2 N3 O7 1-'

? ? ? ? _chemical_formula_moiety?? 'C12 H16 N2 O6, 5(H2 O1)'

? ? ? ? _chemical_formula_moiety?? '(Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O)'

? ? ? ? 諸如'[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H'和'(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2'的分子式寫(xiě)在_chemical_formula_moiety條目是錯(cuò)誤的。

? ? ? ? 但這種格式的分子式可在如下條目中給定：

? ? ? ? _chemical_formula_IUPAC???? '[Co Re (C12 H22 P)2 (C O)6].0.5(C H3 O H)'

? ? ? ? _chemical_formula_structural?? '(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2'

? ? ? ? 若按正確格式給定了_chemical_formula_moiety，但一個(gè)或多個(gè)部分中的原子數(shù)與所有部分所計(jì)算出的總和有差異。則檢查_(kāi)chemical_formula_moiety和_chemical_formula_sum中是否存在印刷錯(cuò)誤，并且已經(jīng)正確解釋了結(jié)構(gòu)中存在的實(shí)際部分。

? ? ? ? _chemical_formula_moiety和_chemical_formula_sum都必須與存在的真實(shí)物質(zhì)相對(duì)應(yīng)，包括任何溶劑，如果由于省略少數(shù)H原子或溶劑原子而引起差異，則不對(duì)應(yīng)于模型所暗示的內(nèi)容。

? ? ? ? 若存在多個(gè)組分例如溶劑，或者其中一個(gè)組分具有無(wú)序或關(guān)于晶體學(xué)對(duì)稱元素?zé)o序，則要確保在計(jì)算Z值、_chemical_formula_moiety 和_chemical_formula_sum時(shí)各組分的比例為正確且允許的。

對(duì)于(2)

? ? ? ? ? "There is a discrepancy between the atom counts in the _chemical_formula_sum and the formula from the _atom_type* data."

? ? ? ? 從Z * _chemical_formula_sum 計(jì)算出的單胞中每個(gè)元素的總數(shù)與如下循環(huán)結(jié)構(gòu)中給出的總數(shù)之間存在差異：

? ? ? ? loop_

? ? ? ? ?? _atom_type_symbol

? ? ? ? ?? _atom_type_description

? ? ? ? ?? _atom_type_number_in_cell

? ? ? ? 檢查_(kāi)cell_formula_units_Z、_chemical_formula_sum以及上述循環(huán)條目是否正確及完整給定。_chemical_formula_sum必須與存在的不同部分中的所有元素的真實(shí)總和相對(duì)應(yīng)，包括任何溶劑和所有氫原子，如果由于省略少數(shù)H原子或溶劑原子而引起差異，則不對(duì)應(yīng)于模型所暗示的內(nèi)容。類似地，atom_type_*循環(huán)必須指示整個(gè)單胞中預(yù)期存在的每種元素類型的總數(shù)，包括所有溶劑和氫原子。

? ? ? ? 若存在多個(gè)組分例如溶劑，或者其中一個(gè)組分具有無(wú)序或關(guān)于晶體學(xué)對(duì)稱元素?zé)o序，則要確保在計(jì)算Z值和_chemical_formula_sum時(shí)各組分的比例為正確且允許的。

? ? ? ? _chemical_formula_sum也必須為正確格式(例如不能使用下標(biāo)格式：C10 H20為正確格式，C~10~ H~20~為錯(cuò)誤格式)。

對(duì)于(3)

? ? ?? ? "There is a discrepancy between the atom counts in the _chemical_formula_sum and the formula from the _atom_site* data."

? ? ? ? 從_chemical_formula_sum和_atom_site_列表(即原子坐標(biāo)列表)得出的原子數(shù)之間存在差異。檢查_(kāi)chemical_formula_sum是否正確給出且格式正確(例如不能使用下標(biāo)格式：C10 H20為正確格式，C~10~ H~20~為錯(cuò)誤格式)。

? ? ? ? 當(dāng)然，_chemical_formula_sum必須與所有存在的不同部分的元素的真實(shí)總和相對(duì)應(yīng)，包括任何溶劑和所有氫原子，如果由于省略少數(shù)H原子或溶劑原子而引起差異，則不對(duì)應(yīng)于模型所暗示的內(nèi)容。在這種情況下，可以忽略此消息。但是，請(qǐng)確保模型確實(shí)是完整的，并且沒(méi)有元素指認(rèn)錯(cuò)誤。

? ? ? ? 若存在多個(gè)組分例如溶劑，或者其中一個(gè)組分具有無(wú)序或關(guān)于晶體學(xué)對(duì)稱元素?zé)o序，則要確保在計(jì)算Z值和_chemical_formula_sum時(shí)各組分的比例為正確且允許的。

? ? ? ? 但是，此警告也可能表明模型中存在被忽略的錯(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。

? ? ? ? 同樣要檢查原子位置占有率是否正確對(duì)應(yīng)于原子坐標(biāo)，否則可能遇到不匹配[例如一個(gè)位于二重軸上的原子通常位置占有率為1.0(但多重?cái)?shù)為0.5)]。此外，當(dāng)考慮到所有可替代的無(wú)序位置時(shí)，無(wú)序原子的占有率總和為1.0。

警告原因：分子式不對(duì)或分子式格式不對(duì)。

解決策略：按上述藍(lán)字部分檢查并改正。