CheckCIF-SYMOP01

PROC-NAME: SYMOP01 Type_1

PURPOSE: To check that the symmetry operators are given in the correct CIF format.

PROCEDURE:

EXTRACT the symmetry operators for each of the following datanames.

_geom_bond_site_symmetry_1, _geom_bond_site_symmetry_2

_geom_contact_site_symmetry_1, _geom_contact_site_symmetry_2

_geom_angle_site_symmetry_1, _geom_angle_site_symmetry_2, _geom_angle_site_symmetry_3

_geom_torsion_site_symmetry_1, _geom_torsion_site_symmetry_2, _geom_torsion_site_symmetry_3, _geom_torsion_site_symmetry_4

_geom_hbond_site_symmetry_D, _geom_hbond_site_symmetry_H, _geom_hbond_site_symmetry_A

TEST

If the symmetry operator is not of the form defined in the CIF dictionary (e.g. 1_555, 3) then

issue ALERT A

   "Alert A Wrong symmetry operator for _geom_bond_site_symmetry_2"

The correct form for the symmetry code is described below. The most common error is the use of symmetry codes such as those used in PLATON (of the form 54502).

The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows:

n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z It must match a number given in _space_group_symop_id. k, l and m refer to the translations that are subsequently applied to the symmetry-transformed coordinates to generate the atom used in calculating the bond. These translations (x, y, z) are related to (k, l, m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided.

Examples:

.              no symmetry or translation to site

4             4th symmetry operation applied

7_645     7th symm. posn.; +a on x; -b on y

(http://journals.iucr.org/services/cif/checking/SYMOP_01.html)

警告原因：对称操作码格式不正确。

解决策略：一般不会出现，重新精修生成CIF文件。