CheckCIF-PLAT031-040

PLAT031 Type_4 Check need for Extinction Correction Parameter

This test checks whether a refined extinction parameter is meaningful i.e. whether its value is significantly larger than its corresponding s.u. If not, this parameter should be removed from the model and the structure refined without this meaningless additional parameter. The current default gives a warning when its value is within 3.33 s.u. SHELXL97-2 will not allow negative values leading to ill-convergence and non-zero maximum shift/error values: remove extinction parameter from the refinement.

(http://journals.iucr.org/services/cif/checking/PLAT031.html)

例：PLAT031_ALERT_4_A Refined Extinction Parameter within Range ...... 0.00 Sigma

警告原因：消光系数误差较大，系数值小于3.33倍的误差，消光系数无意义。

解决策略：删除EXTI命令再精修即可。

PLAT032 Type_4 Check s.u. Flack Parameter

Check the validity of the absolute structure determination. A high s.u. indicates that the experimental data do not support the determination of the absolute structure. This will generally be the case with light atom MoKa data where f" is nearly zero.

Note: Use the TWIN & BASF 0.0 instructions in SHELXL97. The default FLACK parameter is not always reliable, in particular when strongly correlated with the position of the origin (e.g. along y in space-group P21). Please refer to Flack, H.D. & Bernardinelli, G. (1999) Acta Cryst. A55, 908-915 and (2000) J. Appl. Cryst., 33, 1143-1148.

(http://journals.iucr.org/services/cif/checking/PLAT032.html)

警告原因：检查绝对构型的确定结果的正确性。当Flack系数的误差值高时表明试验数据无法支持绝对构型的确定结果。一般来说都是由于使用了Mo靶进行衍射试验且分子中没有重原子(小于Si元素)，导致误差值过大。

解决策略：1. 如果有手性且有重原子，那在修正中加入Flack指令，修正后重新产生CIF。

2. 如果没有手性，或有手性但用Mo靶做仅含小于Si元素的结构，则可将_chemical_absolute_configuration项后面的值改成句点“.”或'unk'(或unknown)。

PLAT033 Type_4 Check Flack Parameter value

Check the relevance/validity of the absolute structure determination. Please refer to Flack, H.D. & Bernardinelli, G. (1999) Acta Cryst. A55, 908-915 and (2000) J. Appl. Cryst., 33, 1143-1148. A value of the Flack parameter that deviates significantly from zero (taking into account the associated s.u.) might indicate that the absolute structure should be inverted in case of a value closer to 1.0 than to zero. A value close to 0.5 may be indicative of an inversion twin or a missed centre of inversion. For valid absolute structure assignments, abs(x) should be less than 2 * s.u., with s.u. < 0.04. For enantiopure compounds, s.u. should be less than 0.1.

(http://journals.iucr.org/services/cif/checking/PLAT033.html)

警告原因：检查Flack系数值的正确性，当Flack系数值远不为0时可能表明需要将绝对构型翻转从而使Flack由1改变为接近于0。当Flack系数值接近0.5时表明该晶体可能为倒反孪晶或者该模型缺失对称中心。当Flack系数值小于2倍的误差值，且误差值小于0.04时，可以确定绝对构型。当为光学纯化合物时，误差值应小于0.1.

解决策略：当Flack系数值约为1时，可以使用inv –f(Olex2中)命令翻转构型。当Flack系数约为0.5时，可以采用Platon升高空间群或者TWIN指令进行孪晶精修。

PLAT034 Type_1 Check for Flack parameter value specified Z>Si, non-centro

No Flack parameter value given for non-centrosymmetric structure with heaviest atom Z > Si. This might be intentional.

(http://journals.iucr.org/services/cif/checking/PLAT034.html)

警告原因：非中心对称结构中存在重原子，却未给出Flack系数值。

解决策略：一般不会出现，重新精修生成CIF文件即可。

PLAT035 Type_1 Check for _chemical_absolute_configuration

Options are 'rm', 'ad', 'rmad', 'syn', 'unk' or '.'

rm   : absolute configuration established by the structure determination of a compound containing a chiral reference molecule of known absolute configuration.

ad   : absolute configuration established by anomalous dispersion effects in diffraction measurements on the crystal.

rmad : absolute configuration established by the structure determination of a compound containing a chiral reference molecule of known absolute configuration and confirmed by anomalous dispersion effects in diffraction measurements on the crystal.

syn  : absolute configuration has not been established by anomalous dispersion effects in diffraction measurements on the crystal. The enantiomer has been assigned by reference to an unchanging chiral centre in the synthetic procedure.

unk  : absolute configuration is unknown, there being no firm chemical evidence for its assignment to hand and it having not been established by anomalous dispersion effects in diffraction measurements on the crystal. An arbitrary choice of enantiomer has been made.

.    : inapplicable.

(http://journals.iucr.org/services/cif/checking/PLAT035.html)

例：PLAT035_ALERT_1_A No _chemical_absolute_configuration info given . ?

警告原因：空间群为非对称中心空间群，未给出绝对构型确定的方法。确定绝对构型的常见方法有如下方式。

rm：绝对构型由带有手性中心的参考分子给出。

ad：绝对构型由反常散射效应确定。

rmad：绝对构型由参考分子和反常散射共同确定。

syn：未通过反常散射确定，手性中心在合成过程中未发生改变。

unk：绝对构型未知，现有试验结果下无法确定绝对构型。CIF中构型选择是任意的。

.：不可用。

解决策略：根据需要选择绝对构型的确定方式，非手性空间群改成句点。手性空间此项后改成ad，非手性空间群改成na。

PLAT036 Type_1 Check for missing Flack Parameter s.u.

No standard uncertainty found for the Flack parameter. When the structure refinement was done with SHELXL97-2, the likely reason for this is a missing BASF instruction. This applies in particular when the associated Flack parameter has the value 0.000. No valid conclusions on the absolute structure can be drawn in that case.

(http://journals.iucr.org/services/cif/checking/PLAT036.html)

警告原因：Flack值未给出误差，此种情况下绝对构型结果不可信。当采用ShelXL97精修时，可能是缺少了BASF命令，尤其是Flack值为0.000时。

解决策略：一般不会出现，重新精修生成cif文件即可。当使用TWIN指令进行精修时，需要加上BASF指令。

PLAT037 Type_1 Check _diffrn_reflns_theta_full

No information is given about the theta value for which the dataset is complete, subject to the percentage given with the dataname _diffrn_measured_fraction_theta_full.

(http://journals.iucr.org/services/cif/checking/PLAT037.html)

警告原因：CIF中缺少_diffrn_reflns_theta_full项，该项受_diffrn_measured_fraction_theta_full约束。

解决策略：一般不会出现，重新精修生成CIF文件即可。

PLAT038 Type_1 Check _diffrn_measured_fraction_theta_max

This fraction should be specified in combination with the theta value given with the dataname _diffrn_reflns_theta_full.

(http://journals.iucr.org/services/cif/checking/PLAT038.html)

警告原因：CIF中缺少_diffrn_measured_fraction_theta_max值。

解决策略：一般不会出现，重新精修生成CIF文件即可。

PLAT039 Type_1 Check _diffrn_measured_fraction_theta_full

This fraction should be specified in combination with the value for _diffrn_reflns_theta_max.

(http://journals.iucr.org/services/cif/checking/PLAT039.html)

警告原因：cif中缺少_diffrn_measured_fraction_theta_full项。

解决策略：一般不会出现，重新精修生成CIF文件即可。

PLAT040 Type_1 Test for H-atoms [0,1]

Alert for 'no H-atoms' in CIF. This is unusual for carbon containing compounds, but may be correct.

(http://journals.iucr.org/services/cif/checking/PLAT040.html)

警告原因：CIF文件中未找到氢原子。

解决策略：将模型加氢并精修即可。如果结构本身不含氢原子，解释即可。