PROC-NAME: CELLZ01 Type_1

PURPOSE: 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).

IF H-M space group mismatches Hall symbol issue General ALERT

? ? ? ? "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:

? ? ? ? The following is the strictly correct way to represent space group 14.

? ? ? ? _symmetry_space_group_name_H-M?? ?'P 1 21/c 1'

? ? ? ? Also interpreted correctly by CHECKCIF is:

? ? ? ? _symmetry_space_group_name_H-M??? 'P 21/c'

? ? ? ? Incorrect are:

? ? ? ? _symmetry_space_group_name_H-M??? 'P 2(1)/c'

? ? ? ? _symmetry_space_group_name_H-M??? 'P 2~1~/c'

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."

(http://journals.iucr.org/services/cif/checking/CELLZ_01.html)

目的：檢查從“_chemical_formula_sum”和“_cell_formula_units_Z”計(jì)算得到的晶胞內(nèi)容與存在于“_atom_site_”列表和“_symmetry_”信息的原子位置信息是否一致。

(1) 對于化學(xué)式總和(_chemical_formula_sum)字符串中的每個(gè)原子種類，用化學(xué)式總和(_chemical_formula_sum)計(jì)數(shù)和晶胞中分子個(gè)數(shù)(_cell_formula_units_Z)來計(jì)算原子數(shù)目。

(2) 對于原子位置(_atom_site_)列表中的原子種類，用原子位置占有率(_atom_site_occupancy)數(shù)值及對稱位點(diǎn)多重性數(shù)值(由NSYM產(chǎn)生)來計(jì)算晶胞中的原子數(shù)目。

若(1)中的原子計(jì)數(shù)與原子類型(_atom_type_)列表(若存在)中聲明的那些不同，發(fā)布一般警告

? ? ? ? "WARNING: Cell contents from the formula and atom_type data differ!"

? ? ? ? 晶胞中由Z和化學(xué)式總和(_chemical_formula_sum)的乘積得出的每種元素的總數(shù)與循環(huán)結(jié)構(gòu)中給出的數(shù)值存在差異：

? ? ? ? loop_

? ? ? ? _atom_type_symbol

? ? ? ? _atom_type_description

? ? ? ? _atom_type_number_in_cell

? ? ? ? 檢查晶胞中分子個(gè)數(shù)(_cell_formula_units_Z)、化學(xué)式總和(_chemical_formula_sum)以及上述循環(huán)結(jié)構(gòu)中的各個(gè)條目是否正確并完整地給出?；瘜W(xué)式總和(_chemical_formula_sum)必須與存在的所有不同片段中所有元素的真實(shí)和相一致，包括任何溶劑以及所有H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)組分具有無序或關(guān)于晶體學(xué)對稱元素?zé)o序，則要確保在計(jì)算Z值和化學(xué)式總(_chemical_formula_sum)時(shí)各組分的比例為正確且允許的。

? ? ? ? 化學(xué)式總(_chemical_formula_sum)必須使用正確的格式(例如不要使用下標(biāo)格式：C10 H20是正確的格式；而C~10~ H~20~是錯誤的格式)。

若H-M空間群與Hall符號不匹配，發(fā)布一般警告

? ? ? ? "Input H-M symbol mismatch with Hall symbol"

? ? ? ? 檢查Hermann–Mauguin空間群符號(_symmetry_space_group_name_H-M)項(xiàng)和Hall空間群符號(_symmetry_space_group_name_Hall)項(xiàng)給出的詞條是否引用相同的空間群和設(shè)置，并且沒有排版錯誤。注意Hermann–Mauguin空間群符號(_symmetry_space_group_name_H-M)項(xiàng)中的空間群符號不應(yīng)包括排版格式(例如下標(biāo)等)。

? ? ? ? 例：

? ? ? ? 以下是空間群14的嚴(yán)格正確的表示。

? ? ? ? _symmetry_space_group_name_H-M??? 'P 1 21/c 1'

? ? ? ? 同樣能夠被CHECKCIF正確識別的是：

? ? ? ? _symmetry_space_group_name_H-M??? 'P 21/c'

? ? ? ? 不正確的是：

? ? ? ? _symmetry_space_group_name_H-M??? 'P 2(1)/c'

? ? ? ? _symmetry_space_group_name_H-M??? 'P 2~1~/c'

若SUMDN大于0.05，發(fā)布一般警告

? ? ? ? "Difference between formula and atom_site contents detected."

若SUMDN小于0.5，發(fā)布一般警告

? ? ? ? "ALERT: Check formula stoichiometry or atom site occupancies."

? ? ? ? 從化學(xué)式總和(_chemical_formula_sum)與原子位置(_atom_site_)列表(即原子坐標(biāo)列表)導(dǎo)出的原子計(jì)數(shù)存在差異。檢查化學(xué)式總和(_chemical_formula_sum)是否正確給出，格式是否正確(例如不要使用下標(biāo)格式：C10 H20為正確格式；C~10~ H~20~為錯誤格式)。

? ? ? ? 當(dāng)然，化學(xué)式總和(_chemical_formula_sum)必須與存在的所有不同片段中所有元素的真實(shí)和相一致，包括任何溶劑以及所有H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，務(wù)必確保模型確實(shí)是完全的并且沒有元素指認(rèn)錯誤。

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

? ? ? ? 化學(xué)式總和(_chemical_formula_sum)必須使用正確的格式(例如不要使用下標(biāo)格式：C10 H20是正確的格式；而C~10~ H~20~是錯誤的格式)。

? ? ? ? 同樣要檢查原子位置占有率是否正確對應(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序位置時(shí)，無序原子的占有率總和為1.0。

若H原子的DN大于0.5，發(fā)布一般警告

? ? ? ? "WARNING: H atoms missing from atom site list. Is this intentional?"

? ? ? ? H原子必須盡可能地包含在模型中。除非H原子不能被定位，并且其位置不能從幾何角度計(jì)算或預(yù)測。例如，溶劑或配位水上的H原子，或者嚴(yán)重?zé)o序的基團(tuán)或溶劑分子上的H原子。

否則發(fā)布一般警告

? ? ? ? "ALERT: Large difference may be due to symmetry error - see SYMMG tests."

例：CELLZ01_ALERT_1_G Difference between formula and atom_site contents detected.

CELLZ01_ALERT_1_G ALERT: Large difference may be due to a symmetry error - see SYMMG tests

? ? ? ? From the CIF: _cell_formula_units_Z?? ??6

? ? ? ? From the CIF: _chemical_formula_sum ??C65 H65 B0.67 F2.67 Fe N Ni O P4

? ? ? ? TEST: Compare cell contents of formula and atom_site data

? ? ? ? atom? ??Z*formula? ? cif sites? ? diff

? ? ? ? C? ? ? ? ?390.00? ? ? ? ?390.00? ? ?0.00

? ? ? ? H? ? ? ? ?390.00? ? ? ? ?390.00? ? ?0.00

? ? ? ? B? ? ? ? ?4.02? ? ? ? ? ? ?6.00? ? ? ? ?-1.98

? ? ? ? F? ? ? ? ?16.02? ? ? ? ? ?24.00? ? ? ?-7.98

? ? ? ? Fe? ? ? ??6.00? ? ? ? ? ? 6.00? ? ? ? ?0.00

? ? ? ? N? ? ? ? ?6.00? ? ? ? ? ? 6.00? ? ? ? ? 0.00

? ? ? ? Ni? ? ? ??6.00? ? ? ? ? ? 6.00? ? ? ? ? 0.00

? ? ? ? O? ? ? ? ?6.00? ? ? ? ? ? 6.00? ? ? ? ?0.00

? ? ? ? P? ? ? ? ?24.00? ? ? ? ? ?24.00? ? ? ?0.00

? ? ? ? S? ? ? ? ?18.00? ? ? ? ? ?18.00? ? ? ?0.00

警告原因：分子式和Z值沒有給對。

解決策略：在ins里給對分子式和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。