menucheckCIF procedure
PROC-NAME: STRVAL_02PURPOSE: To check that _refine_ls_abs_structure_rogers is within expected limits.
PROCEDURE:
ROGERS = _refine_ls_abs_structure_rogers
TEST
IF ABS(ROGERS) > 1.2 issue ALERT C
"Alert C Rogers value is too large"
| The value of _refine_ls_abs_structure_rogers is well outside the expected range of -1.0 to 1.0. This may mean that there is some systematic error in the model or data, or that the Rogers parameter is meaningless because the compound is a weak anomalous scatterer (i.e. no atom heavier than Si is present). In the latter case, it is best to remove the Rogers 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_rogers is still out of range, the quality of the data and/or the correctness of the model could be checked carefully. |
"Alert C Rogers value is inconclusive"
|
The correct absolute structure has been defined by the atomic
coordinates if _refine_ls_abs_structure_rogers is close to 1.0
(range -1.0 to 1.0)
In cases of intermediate values of _refine_ls_abs_structure_rogers, 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 _refine_ls_abs_structure_rogers is essentially meaningless because the compound is a weak anomalous scatterer (i.e. no atom heavier than Si is present). If the value for _refine_ls_abs_structure_rogers is meaningless because the compound is a weak anomalous scatterer, it is best to remove _refine_ls_abs_structure_rogers from the CIF. This will usually be the case if no atom heavier than Si is present. If the value for _refine_ls_abs_structure_rogers is meaningful and a heavy atom is present, 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. Please also provide appropriate reference details under _refine_ls_abs_structure_details. For example: _refine_ls_abs_structure_details 'Rogers (1981), 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 Rogers value is too low"
| The value of _refine_ls_abs_structure_rogers is well outside the expected range of -1.0 to 1.0. This may mean that there is some systematic error in the model or data, or that the Rogers parameter is meaningless because the compound is a weak anomalous scatterer (i.e. no atom heavier than Si is present). In the latter case, it is best to remove the Rogers 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_rogers is still out of range, the quality of the data and/or the correctness of the model could be checked carefully. |
"Alert C Rogers value suggests reverse chirality"
|
The correct absolute structure has been defined by the atomic
coordinates if _refine_ls_abs_structure_rogers is close to 1.0
(range -1.0 to 1.0). If _refine_ls_abs_structure_rogers 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_rogers, a merohedral twin or a partial mix of enantiomers may be present and this fact should be discussed in the manuscript. Choose the configuration that gives the value of _refine_ls_abs_structure_rogers closest to 1.0. However, intermediate values might also be obtained when _refine_ls_abs_structure_rogers is essentially meaningless because the compound is a weak anomalous scatterer (i.e. no atom heavier than Si is present). If the value for _refine_ls_abs_structure_rogers is meaningless because the compound is a weak anomalous scatterer, it is best to remove _refine_ls_abs_structure_rogers from the CIF. This will usually be the case if no atom heavier than Si is present. If the value for _refine_ls_abs_structure_rogers is meaningful and a heavy atom is present, 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. Please also provide appropriate reference details under _refine_ls_abs_structure_details. For example: _refine_ls_abs_structure_details 'Rogers (1981), 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).] |
