menucheckCIF procedure
PROC-NAME: STRVAL_01 (FL)PURPOSE: To check that _refine_ls_abs_structure_flack is within expected limits.
PROCEDURE:
FLACK = _refine_ls_abs_structure_flack
SFLACK = su of _refine_ls_abs_structure_flack
TEST
IF FLACK > 0.7 issue ALERT C
"Alert C Chirality of atom sites is inverted?"
|
The correct absolute structure has been defined by the atomic
coordinates if _refine_ls_abs_structure_flack is close to 0.0
(and the s.u. is sufficiently small).
If _refine_ls_abs_structure_flack is close to 1.0, the
incorrect enantiomer is being modelled and the atomic coordinates
should be inverted and refined again.
In cases of intermediate values of _refine_ls_abs_structure_flack, and you believe that a merohedral twin or a partial mix of enantiomers is present, choose the configuration that gives the lowest value for _refine_ls_abs_structure_flack. Note that if the s.u. of the Flack parameter is large, e.g. greater than or equal to 0.3, one cannot confidently derive the absolute structure from the data, because, within the 3sigma confidence limits, the full range of possible values of the Flack parameter are plausible. In such cases, even if the Flack parameter itself is close to 0.0, no conclusions about the absolute structure are justified. This will usually be the case if the compound is a weak anomalous scatterer (i.e. no atom heavier than Si is present). If a heavy atom is present, but the s.u. is still large, you should ensure that a significant fraction (ideally all) of the Friedel opposites of the symmetry unique reflections have been included in the data set. If the absolute structure parameter is meaningless because the compound is a weak anomalous scatterer, it is best to remove the absolute structure parameter from the CIF. If the absolute structure parameter is meaningful, please also provide appropriate reference details under _refine_ls_abs_structure_details. For example: _refine_ls_abs_structure_details 'Flack (1983), XXXX Friedel pairs' and replace the XXXX with the actual number of Friedel pairs used in the refinement. [An easy way to determine the number of Friedel pairs is to look at the difference between the number of unique reflections used in SHELXL when a MERG2 and MERG 3 instruction is used (MERG 3 forces Friedel pairs to be merged before use).] |
"Alert C Flack test results are ambiguous."
|
The correct absolute structure has been defined by the atomic
coordinates if _refine_ls_abs_structure_flack is close to 0.0
(and the s.u. is sufficiently small).
In cases of intermediate values of _refine_ls_abs_structure_flack, a merohedral twin or a partial mix of enantiomers may be present and this fact should be discussed in the manuscript. However, intermediate values might also be obtained when the absolute structure parameter is essentially meaningless because the compound is a weak anomalous scatterer. Note that if the s.u. of the Flack parameter is large, e.g. > 0.3, one cannot confidently derive the absolute structure from the data, because, within the 3sigma confidence limits, the full range of possible values of the Flack parameter are plausible. In such cases, even if the Flack parameter itself is close to 0.0, no conclusions about the absolute structure are justified. This will usually be the case if the compound is a weak anomalous scatterer (i.e. no atom heavier than Si is present). If a heavy atom is present, but the s.u. is still large, you should ensure that a significant fraction (ideally all) of the Friedel opposites of the symmetry unique reflections have been included in the data set. If the absolute structure parameter is meaningless because the compound is a weak anomalous scatterer, it is best to remove the absolute structure parameter from the CIF. If the absolute structure parameter is meaningful, please also provide appropriate reference details under _refine_ls_abs_structure_details. For example: _refine_ls_abs_structure_details 'Flack (1983), XXXX Friedel pairs' and replace the XXXX with the actual number of Friedel pairs used in the refinement. [An easy way to determine the number of Friedel pairs is to look at the difference between the number of unique reflections used in SHELXL when a MERG2 and MERG 3 instruction is used (MERG 3 forces Friedel pairs to be merged before use).] |
"Alert C Flack parameter is too small."
| The value of _refine_ls_abs_structure_flack is well outside the expected range of 0.0-1.0. This may mean that there is some systematic error in the model or data, or that the absolute structure parameter is meaningless because the compound is a weak anomalous scatterer. In the latter case, the s.u. of the Flack parameter is also usually large and it is best to remove the absolute structure parameter from the CIF. If a heavy atom is present in the compound, you should ensure that a significant fraction (ideally all) of the Friedel opposites of the symmetry unique reflections have been included in the data set. If _refine_ls_abs_structure_flack is still out of range, the quality of the data and/or the correctness of the model could be checked carefully. |
"Alert C Flack test results are meaningless."
|
If the s.u. of the Flack parameter is large, e.g. > 0.3,
one cannot confidently derive the absolute structure from the data,
because, within the 3sigma confidence limits, the full range of
possible values of the Flack parameter are plausible. In such cases,
even if the Flack parameter itself is close to 0.0, no conclusions
about the absolute structure are justified. This will usually be
the case if the compound is a weak anomalous scatterer (i.e. no
atom heavier than Si is present). If a heavy atom is present,
but the s.u. is still large, you should ensure that a significant
fraction (ideally all) of the Friedel opposites of the symmetry
unique reflections have been included in the data set.
If the absolute structure parameter is meaningless because the compound is a weak anomalous scatterer, it is best to remove the absolute structure parameter from the CIF. |
