|
_chemical_formula_moiety has the identical format to _chemical_formula_sum,
namely C, H, then alphabetical, with the exception that the individual
unconnected independent entities in the structure are listed separately.
A common mistake is to attempt to depict organometallic coordination with
this entry. Such coordination can be given under
_chemical_formula_structural or _chemical_formula_IUPAC if desired, but
must never be given as _chemical_formula_moiety. Furthermore, do not
use subscript formatting: C10 H20 is correct, C~10~ H~20~ is not. Nesting
of parentheses is also not allowed.
Correct examples:
Formulae like '[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H' and
'(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2' are INCORRECT for
_chemical_formula_moiety. If _chemical_formula_moiety has been given in the correct style, then there is a discrepancy between the atom counts in one or more of the moieties and the total calculated over all moieties. Check that there is not a typographical error in _chemical_formula_moiety and _chemical_formula_sum and that the actual moieties present in the structure have been interpreted correctly. Both _chemical_formula_moiety and _chemical_formula_sum must correspond with the true species present, including any solvent, 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, _chemical_formula_moiety and _chemical_formula_sum. |
|
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. Similarly, the atom_type_* loop must indicate the total number of each element type expected to be present in the entire unit cell, including all solvent and H 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). |
|
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. However, this alert could also be an indication of overlooked errors in the model. Be sure that the model is indeed as complete as intended and that no elements have been misassigned. 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 _diffrn_radiation_type is not identified,
issue a General ALERT
"Radiation type not identified. Calculation of
_exptl_absorpt_correction_mu not performed."
|
Only Mo, Cu and Ag radiation is recognized by CHECKCIF; wavelengths
from other X-ray tubes, synchrotrons or neutrons will cause the
calculation of _exptl_absorpt_correction_mu to be skipped.
If you are using Mo, Cu or Ag radiation, but this is not recognised, the format of your keyword entry for _diffrn_radiation_type may be incorrect. The correct format for _diffrn_radiation_type is 'Mo K\a', 'Cu K\a' or 'Ag K\a'. |
|
This alert does not imply that you need to apply an absorption
correction or that your absorption correction is inappropriate
in any way. It indicates that your value of the linear absorption
coefficient (_exptl_absorpt_correction_mu) in the CIF does not
agree with the value calculated from your given unit cell volume
and the total number of each element type in the unit cell.
Small differences between your value and the predicted value may arise if your software uses an older (e.g. Int. Tables, Vol. IV, 1974) or a different source of the mass attenuation coefficients. CHECKCIF uses the photon interaction cross sections for the elements given in Int. Tables, Vol. C, 1992, Table 4.2.4.2, pp. 193-198. Other differences between your value and the predicted value will arise if the unit cell volume, Z or _chemical_formula_sum in your CIF is different from that used to obtain your value of mu. Don't forget that _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, _chemical_formula_sum and the linear absorption coefficient. |
|
Use ONLY one of the specified keywords and no other text under
_exptl_absorpt_correction_type. Note that psi-scans should be
indicated as 'psi-scan' and not as '\f-scan'. The citation should
be in parentheses in the usual citation format.
Example: |
|
A literature citation to the absorption correction method must
be provided. However, do not append this to the keyword given
with _exptl_absorpt_correction_type. There is a separate data
name entry for the citation which is _exptl_absorpt_process_details.
The citation should be in parentheses in the usual citation format.
Example: |
| Check that the temperature has been given in the correct units, i.e. Kelvin. |
|
The minimum theta value cannot exceed the maximum value. Either
there is a typographical error or the values under
_cell_measurement_theta_min and _cell_measurement_theta_max have
accidentally been reversed. |
| There is a discrepancy between the unit cell volume given in the CIF and that calculated from the unit cell dimensions given in the CIF. Check the volume and cell dimensions for typographical errors. |
| There is a discrepancy between the standard uncertainty (s.u.) for the unit cell volume given in the CIF and that calculated from the s.u.s of the unit cell dimensions given in the CIF. Check the volume and cell dimension s.u.s for typographical errors (rule of '19' applies). |
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). |
|
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:
Also interpreted correctly by CHECKCIF is:
Incorrect are: |
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."
|
The _chemical_formula_sum must contain just one sequence of
elements (i.e. not separated into moieties) in the order
C, H, then alphabetical. Do not use any special formatting
characters, such as subscripts (e.g. C10 H20 is correct,
C~10~ H~20~ is not). There is no space between an element and
its count, but there is a space before the next element.
Enclose the string in quotes.
Example: |
|
The formula weight given in the CIF differs from that calculated using
the formula in _chemical_formula_sum. Check that (a) you have calculated
the formula weight correctly and (b) that _chemical_formula_sum is
correctly and fully specified. Remember that _chemical_formula_sum and
_chemical_formula_weight 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, _chemical_formula_sum and the formula weight. _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). |
|
The formula weight given in the CIF differs from that calculated using
the _atom_site_ list (i.e. the list of atomic coordinates). Check that
you have calculated the formula weight correctly and that it corresponds
with the true sum of all elements in all distinct moieties present,
including any solvent and all H atoms. This message can be ignored if
the model is intentionally incomplete 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 _chemical_formula_weight. However, this alert could also be an indication of overlooked errors in the model. Be sure that the model is indeed as complete as intended and that no elements have been misassigned. 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. Similarly, this alert could appear if you have given the following loop structure:
loop_ A discrepancy between the formula weight derived from this list and the formula weight given under _chemical_formula_weight may mean that the atom counts in the loop are incorrect or that _chemical_formula_weight has been incorrectly specified. Once again, _atom_type_symbol and _atom_type_number_in_cell must correspond with the true contents of the unit cell, including any solvent and all H atoms. |
IF A word has been used that has not been identified as a standard identifier issue ALERT C
"Alert C The word below has not been recognised as a standard
identifier."
IF No recognised colour has been given for crystal colour issue ALERT C
"Alert C No recognised colour has been given for crystal colour."
IF The identifiers are ordered incorrectly issue ALERT C
"Alert C There is an ordering error in _exptl_crystal_colour.
It should be (QUALIFIER) (INTENSITY) (BASE_COLOUR)."
|
_exptl_crystal_colour must be given as a set of specific keywords in the
following specific order:
(QUALIFIER) (INTENSITY) (BASE_COLOUR) where (QUALIFIER) and/or (INTENSITY) are optional. These keywords must be chosen from the following list: (qualifier) blank, metallic, lustrous, translucent, fluorescent, clear (intensity) blank, dark, light, intense, pale (base-colour) white, black, blue, violet, red, pink, yellow, gold, silver, bronze, grey, orange, green, colourless, brown, purple |
| _exptl_crystal_size_rad is not given in the CIF although _exptl_crystal_description is given as 'cylinder' or 'sphere'. Either give the cylinder or sphere radius or change _exptl_crystal_description to another type. |
| The magnitudes of the crystal dimensions do not match the min, mid and max definitions. This is usually caused by a typographical error when entering the crystal dimensions or assigning the greatest dimension to the _exptl_crystal_size_min entry and vice versa. |
|
The crystal must be smaller than size of the incident beam at the
crystal. For most diffractometers with fine-focus X-ray tubes and
monochromated radiation, this size is unlikely to be much greater
than 0.5 mm. Note that increasing the collimator diameter will not
necessarily increase the size of the incident beam at the crystal.
If the crystal used in the data collection is larger than the
incident beam, then unpredictable errors in intensities will occur
due to the varying amounts of the crystal in the beam for different
reflection positions. If you obtain an alert about crystal size,
then data should be collected with a smaller crystal. For the
above reasons, it is recommended that crystals be generally smaller
than 0.5 mm along any edge.
If you used neutrons and obtained an alert about the crystal size, then you have forgotten to set _diffrn_radiation_type 'neutron'. |
|
The calculated density given in the CIF differs from that
calculated using the specified formula weight and the stated number of
formula units in the unit cell (Z). Check that (a) you have calculated
the density correctly and (b) that _chemical_formula_weight and
_cell_formula_units_Z are correctly specified. Remember that
_chemical_formula_weight and the calculated density 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_weight. |
|
You have given the method used to determine the density of the crystal
under _exptl_crystal_density_method, but have forgotten to specify the
experimentally measured density under _exptl_crystal_density_meas.
If you have not actually determined the density experimentally, then
set _exptl_crystal_density_method to 'not measured'.
The experimentally measured density should not be confused with the calculated density derived from the unit cell volume and contents which should be specified under _exptl_crystal_density_diffrn. |
| The calculated density given in the CIF differs significantly from the experimentally measured density quoted in the CIF. Check that you have measured, calculated and entered the densities correctly and that in your calculations you have allowed correctly for 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. |
| You have given the minimum residual electron density with a value greater than the maximum residual electron density. Check that you have not accidentally reversed these values, and that you have not forgotten the negative sign for the minimum residual electron density. |
|
The minimum residual electron density is more negative
than normally expected, even after making an allowance for the
heaviest element in the structure. This is often an indication
that (a) the absorption corrections are inadequate; (b) the overall
quality of the data may be poor, leading to spurious peaks and holes
of residual electron density; (c) there is twinning which has not
been allowed for where overlap from the second twin domain (which may
have been ignored in the data collection) causes errors in the
intensities of some reflections; (d) the model is incorrect or incomplete
in terms of incorrect element assignment, missing atoms or unmodelled
or inadequately modelled disorder or solvent atoms.
If you believe you have eliminated all potential causes of this alert, but the minimum residual electron density still remains more negative than normally expected, you must specify the name of the nearest atom to this minimum and its distance from the minimum. |
| The minimum residual electron density should have a negative value. Have you forgotten the sign or reversed the minimum and maximum entries? |
| The minimum residual electron density is more negative than normally expected. Please specify the name of the nearest atom to this minimum and its distance from the minimum. |
|
The maximum residual electron density is larger
than normally expected, even after making an allowance for the
heaviest element in the structure. This is often an indication
that (a) the absorption corrections are inadequate; (b) the overall
quality of the data may be poor, leading to spurious peaks and holes
of residual electron density; (c) there is twinning which has not
been allowed for where overlap from the second twin domain (which may
have been ignored in the data collection) causes errors in the
intensities of some reflections; (d) the model is incorrect or incomplete
in terms of incorrect element assignment, missing atoms or unmodelled
or inadequately modelled disorder or solvent atoms.
If you believe you have eliminated all potential causes of this alert, but the maximum residual electron density still remains larger than normally expected, you must specify the name of the nearest atom to this minimum and its distance from the minimum. |
| The maximum residual electron density should have a positive value. Have you reversed the minimum and maximum entries? |
| The maximum residual electron density is larger than normally expected. Please specify the name of the nearest atom to this maximum and its distance from the maximum. |
_refine_ls_structure_factor_coef must ONLY be one of the following
keywords (do not add extra text to this field - e.g. F-squared
or F^2^ is not correct):
|
_refine_ls_structure_factor_coef must ONLY be one of the following
keywords (do not add extra text to this field - e.g. F-squared
or F^2^ is not correct):
|
|
Ideally, the goodness of fit (or standard deviation of an observation
of unit weight) should be as close to 1.0 as possible. Values
that deviate significantly from 1.0 may be an indication of one of the
following: (a) the model is incorrect or incomplete or
has been inadequately developed to account for disorder or solvent;
(b) the reflection data are poor or weak; (c) there is twinning
which has not been allowed for where overlap from the second twin
domain (which may have been ignored in the data collection) causes
errors in the intensities of some reflections; (d) the absorption
corrections are inadequate; (e) the weighting scheme is inappropriate.
Users of SHELXL should normally obtain goodness of fit values very close to 1.0 if none of the above features is relevant. If this is not the case, check that the weighting scheme co-efficients recommended by the program have been updated immediately prior to the last refinement run. If only the weights proposed when the model was in an early stage of development are used and not subsequently updated, the goodness of fit might deviate significantly from 1.0 and the weights should be updated. Users of other refinement software, particularly older programs or with refinement on F, might routinely obtain values for the goodness of fit in the range 1.5-2.5. This is acceptable, but authors need to be satisfied that this range for the goodness of fit is normal for good structures determined in their laboratory. However, values for the goodness of fit that are significantly smaller than 1.0 are usually a symptom of other problems with the data or model. |
| You are using an "old-fashioned", but still legal data name: _refine_ls_goodness_of_fit_obs. Please update the item to match the currently preferred name of _refine_ls_goodness_of_fit_ref. To ease this problem for the future, it is recommended that you upgrade or modify your CIF generating software accordingly. |
_refine_ls_hydrogen_treatment must ONLY be one of the following
keywords (do not add extra text to this field):
You cannot use multiple keywords to depict a variety of methods - use 'mixed' instead. For a riding refinement, use 'constr'. By default, SHELXL inserts 'mixed' in EVERY case. Please ensure that you edit this item to represent the actual H-atom treatment used. Additional descriptive text, if required, should be placed in the _publ_section_exptl_refinement section. |
|
_diffrn_radiation_type must ONLY be one of the following
keywords (do not add extra text to this field and watch the formatting
e.g. 'Cu K~\a~' and 'Cu Kalpha' are incorrect, the space before K should
be present): 'Cu K\a' 'Mo K\a' 'Ag K\a' neutron synchrotron If you used a less common X-ray source, such as a gold X-ray tube, this alert can be ignored. The keyword 'synchrotron' should be used for all work carried out on a beam line. |
|
Have you used the correct radiation symbol and the corresponding
wavelength? Check for typographical errors, especially if you are
hand editing an old CIF and changed the wavelength, but forgot the
radiation symbol or vice-versa. The K(alpha-bar) wavelength should be used. |
| The multiplier in _reflns_threshold_expression is used to select the significantly intense reflections for use in the calculation of the regular R-factor given in _refile_ls_R_factor_gt. Older refinement programs, particularly those based on F, may use ONLY the intense reflections selected by this criterion. Therefore it is highly desirable to keep the multiplier in _reflns_threshold_expression as small as possible. Typically a value of 2 or less is used in the expressions 'I > 2\s(I)' or 'F^2^ > 2\s(F^2^)', or 4 or less in 'F > 4\s(F)'. |
|
You have not specified _reflns_threshold_expression or the text
cannot be interpreted. This item is compulsory and should be of
the form 'I > x\s(I)' or 'F^2^ > x\s(F^2^)' or 'F > x\s(F)'.
The multiplier, x, is typically 2 or less. If you selected zero for the multiplier, you still must provide the expression for _reflns_threshold_expression; e.g. 'I > 0\s(I)' |
| You are using an "old-fashioned", but still legal data name: _reflns_observed_criterion. Please update the item to match the currently preferred name of _reflns_threshold_expression. To ease this problem for the future, it is recommended that you upgrade or modify your CIF generating software accordingly. |
|
The total number of reflections measured originally by the
diffractometer should be given under _diffrn_reflns_number.
Any subsequent set of reflections derived from this must, logically,
be a subset of the total reflections measured. Therefore, the reported
number of reflections for _reflns_number_gt, i.e. those with
intensity greater than the sigma threshold defined by
_reflns_threshold_expression, must be less than (or possibly equal to)
the number given under _diffrn_reflns_number. Check for typographical errors. |
| You are using an "old-fashioned", but still legal data name: _reflns_number_observed. Please update the item to match the currently preferred name of _reflns_number_gt. To ease this problem for the future, it is recommended that you upgrade or modify your CIF generating software accordingly. |
| Check that you have not accidentally mistyped or reversed one or more of the entries for the maximum and minimum values of h,k,l. Note that the limits for the reflection indices should correspond with the extremes used for the data collection and not those after the data have been merged. |
| The total number of reflections measured originally by the diffractometer should be given under _diffrn_reflns_number. Any subsequent set of reflections derived from this must, logically, be a subset of the total reflections measured. Therefore, the reported number of unique reflections given with _reflns_number_total must be less than (or possibly equal to) the number given under _diffrn_reflns_number. Check for typographical errors. |
|
The total number of symmetry-unique reflections, including all
reflections considered to be "unobserved", but excluding
systematically absent reflections, should be given under
_reflns_number_total. If Friedel-related reflections are being
treated as independent observations in order to utilise the effects
of anomalous dispersion, _reflns_number_total should correspond
with the total number of these independent reflections.
Normally, one uses just these independent reflections
during refinement and any subsequent set of reflections derived from
this must, logically, be a subset of the total unique reflections.
Therefore, the reported number of reflections for _reflns_number_gt,
i.e. those with intensity greater than the sigma threshold defined by
_reflns_threshold_expression, must normally be less than (or possibly
equal to) the number given under _reflns_number_total.
Check for typographical errors and/or that you have merged the equivalent reflections correctly before refinement. An exception to this requirement may occur if data from a non-merohedrally twinned crystal is employed, as this may result in more than one entry in the reflection file for a given set of h,k,l indices (e.g. data read into SHELXL with HKLF 5). As a result, more reflections may be used in the refinement than the apparent number of unique reflections. A second exception might be if you deliberately choose not to merge symmetry equivalent reflections before the refinement. This procedure is not recommended and its use should be specifically mentioned under _publ_section_exptl_refinement. |
| You are using an "old-fashioned", but still legal data name: _reflns_number_observed. Please update the item to match the currently preferred name of _reflns_number_gt. To ease this problem for the future, it is recommended that you upgrade or modify your CIF generating software accordingly. |
NREFRAT = _reflns_number_total / NREF
NREF% = NREFRAT * 100
NFRIED = MAX ( _reflns_number_total - NREF, 0)
NFDRAT = NFRIED / NREF
TEST_1 : Type_1
In the calculation of NREF the maximum and minumum h,k,l indices in the
in the unque portion of reciprocal space are saved. These are compared
with the _diffrn_reflns_limit_ values in the CIF. If the estimated
maximum h,k,l values do not match either the CIF _max or the absolute
_min values issue a General ALERT
"ALERT: Expected hkl max differ from CIF values"
|
The maximum (or minimum) limits of h, k and l given in the CIF do not
correspond with those caclculated using the theta(max) value stated
under _diffrn_reflns_theta_max. Check that theta(max) has been given correctly. If so, it may be that the h,k,l index limits set during the data collection did not correspond correctly with the limits required to ensure that at least all possible unique reflections up to the specified theta(max) were collected. If one or more of the index limits was set to a too small value, truncation of the data will have occurred and the data should be recollected. This problem sometimes occurs, especially with older diffractometers, when the index limits and theta(max) must be set independently by hand and the operator forgets to check both settings. |
IF NREF%
< 85 issue ALERT A
"Alert A: < 85% complete (theta max?)"
< 90 issue ALERT B
"Alert B: < 90% complete (theta max?)"
< 95 issue ALERT C
"Alert C: < 95% complete"
|
The total number of symmetry-unique reflections, including all
reflections considered to be "unobserved", but excluding
systematically absent reflections, should be given under
_reflns_number_total. If Friedel-related reflections are being
treated as independent observations in order to utilise the effects
of anomalous dispersion, _reflns_number_total should correspond
with the total number of these independent reflections.
The expected number of unique reflections is calculated from your reported theta(max). You should first check that theta(max) has indeed been reported correctly. It is essential that, as far as possible, at least all possible unique reflections have been recorded up to the chosen theta(max). Severe deficiencies in this regard should be rectified by recollecting the data. If you do not know why your data are incomplete, it can sometimes be instructive to examine the reflection file by using the ASYM-VIEW option of PLATON (requires the SHELXL format .hkl or .fcf file). This will highlight the missing reflections in each layer of the data. Missing reflections that occur in strips or inner regions of the layers suggest that an incorrect data collection strategy was used or that there was some other problem with the data collection. E.g. incorrect h,k,l limits causing truncation in one or more directions, premature termination of the data collection, loss of X-rays during part of the data collection. One accidental cause of incompleteness is to choose the wrong axis to scan completely with monoclinic space groups (e.g. collecting +h, +/-k, +l reflections when b is the unique axis). Another reason for having incomplete data can be that your (old) data reduction program is discarding reflections with negative intensity, so that only those with positive intensity are retained in the data set and reported under _reflns_number_total. In this case, you should update or replace your data reduction program so that this does not occur. If you are using a serial diffractometer (scintillation counter), there is usually no reason that the data should not be virtually 100% complete and severe incompleteness should be investigated carefully. Low temperature devices can sometimes be a hindrance, but should not lead to a large fraction of incomplete data. With CCD detectors, one must ensure that the data collection strategy is sufficient to cover all unique reflections. An additional scan set at a different chi or omega setting may be required to ensure that the data set is complete. For diffractometers with only one circle (e.g. the fixed phi circle on the Stoe IPDS and Mar Research IP systems, data completeness can be more problematic. One method for mimimising incompleteness is to ensure that the crystal is mounted such that a crystal axis is NOT coincident with the phi axis (i.e. make sure your crystals are mounted in a skew orientation). People who use CCD or IP detectors may find that just the high angle reflections are incomplete. This occurs with rectangular apertures because the corners of the detector will record to higher angles that the mid points of the sides. In such cases it will be found that the data are essentially 100% complete at a lower theta value. This information should be incorporated into the CIF by correctly filling out the following two data items which specify the theta value at which the data are essentially 100% complete and the actual completeness at this theta value:
_diffrn_reflns_theta_full One means of obtaining estimates for the above two items is to use the ACTA instruction in SHELXL, together with its optional parameter. If a value is specified for 2theta on this instruction, this value will be used to correctly fill in the above two entries in the CIF. This does not truncate the data during refinement.
Example:
_diffrn_reflns_theta_max 28.0 |
If the space group is centrosymmetric also test if the expected
reflection count is exceeded (perhaps because symmetry absent or
equivalent reflections were mistakenly counted). Type_3
IF NREF%
> 115 issue ALERT A
"Alert A: > 15% excess reflns - sys abs data present?"
> 110 issue ALERT B
"Alert B: > 10% excess reflns - sys abs data present?"
> 105 issue ALERT C
"Alert C: > 5% excess reflns - sys abs data present?"
|
The total number of symmetry-unique reflections, including all
reflections considered to be "unobserved", but excluding
systematically absent reflections, should be given under
_reflns_number_total. If Friedel-related reflections are being
treated as independent observations in order to utilise the effects
of anomalous dispersion, _reflns_number_total should correspond
with the total number of these independent reflections.
The expected number of unique reflections is calculated from your reported theta(max). You should first check that theta(max) has indeed been reported correctly. Having excess numbers of reflections is an indication that you have not or have incorrectly merged symmetry-equivalent reflections, or that you have included the systematically absent reflections in your count of unique reflections. Check for typographical errors and/or that you have merged the equivalent reflections correctly before refinement. An exception to this requirement may occur if data from a non-merohedrally twinned crystal is employed, as this may result in more than one entry in the reflection file for a given set of h,k,l indices (e.g. data read into SHELXL with HKLF 5). As a result, more reflections may be used in the refinement than the apparent number of unique reflections. A second exception might be if you deliberately choose not to merge symmetry equivalent reflections before the refinement. This procedure is not recommended and its use should be specifically mentioned under _publ_section_exptl_refinement. |
TEST_3 : Type_4
For noncentrosymmetric structures, test if the _reflns_number_total count
includes any Friedel-related reflections, and estimate how may and what
fraction they are of the symmetry-unique count NREF. The test is divided
into "heavy atom" structures (heavier atoms than Si are present) and "light
atom" structures. The light-atom test includes the radiation used in order
to establish if anomalous scattering is sufficient to permit
the reliable determination of the absolute structure.
IF Z > Si .and. NFDRAT < 0.5 issue a General ALERT
"WARNING: Large fraction of Friedel related reflns needed to determine
absolute structure."
|
If the structure is non-centrosymmetric with atoms HEAVIER than silicon
then it is expected that Friedel pairs will be used in the refinement
and that the absolute structure will be determined experimentally,
even if one or more chiral centres in the molecule are already
unambiguously known from the chemistry or synthesis of the compound.
If the heaviest element present is S, P or Cl, then it is strongly
recommended that the Friedel opposites of all symmetry-unique reflections
be included in the data set. The proportion of Friedel related
reflections required decreases with the increasing atomic weight of
the heaviest element that is present, but for medium weight elements,
it is recommended that at least 50% of the potential Friedel
related reflections have been recorded. The more Friedel pairs that are
present in the data set, the smaller will be the s.u. for the absolute
structure parameter (Flack's x).
If the structure is non-centrosymmetric with atoms HEAVIER than Silicon the following two line items must be present in the CIF:
_refine_ls_abs_structure_details Add the number of Friedel pairs used in the refinement to the _refine_ls_abs_structure_details line so that it looks like: _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).] |
IF Z > Si .and. NFDRAT > 0.5 issue a General ALERT
"Please check that the estimate of the number of Friedel pairs is
correct. If it is not, please give the correct count in the
_publ_section_exptl_refinement section of the submitted CIF."
|
If the structure is non-centrosymmetric with atoms HEAVIER than silicon
the following two line items must be present in the CIF:
_refine_ls_abs_structure_details We have estimated the number of Friedel related reflections in your data set from a comparison of your value of _reflns_number_total with the theoretical number calculated for the symmetry-unique portion of reciprocal space out to your stated theta(max). We ask you to check our estimate and correct as necessary. Then add the number of Friedel pairs used in the refinement to the _refine_ls_abs_structure_details line so that it looks like: _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).] |
|
As you only have a light atom structure (heaviest element lighter than
silicon), anomalous dispersion effects are very small, even with Cu
radiation. The reliability of the absolute structure determination will
be improved if as many Friedel pairs of reflections as possible are
present in the data set. Your current data set appears to contain less
than 50% of the total potential Friedel related reflections that are
possible up to your stated theta(max) and the absolute structure
determination is probably unreliable (i.e. the value of the absolute
structure parameter is meaningless because of its large s.u. value).
If you are attempting to draw any conclusions about the absolute structure
from the crystallographic data, then it is strongly recommended that the
Friedel opposites of all symmetry-unique reflections be included in the
data set. A recollection of your data is therefore probably warranted.
If the structure is non-centrosymmetric with only atoms LIGHTER than silicon, but you believe that the crystallographic experiment has successfully determined the absolute structure, the following two line items must be present in the CIF:
_refine_ls_abs_structure_details We have estimated the number of Friedel related reflections in your data set from a comparison of your value of _reflns_number_total with the theoretical number calculated for the symmetry-unique portion of reciprocal space out to your stated theta(max). We ask you to check our estimate and correct as necessary. Then add the number of Friedel pairs used in the refinement to the _refine_ls_abs_structure_details line so that it looks like: _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).] If no useful absolute structure parameter can be refined (i.e. the value of the absolute structure parameter is meaningless because of its large s.u. value), authors should consider merging Friedel-pair reflections before final refinement, and stating this in the _publ_section_exptl_refinement section of the CIF, along with the meaningless absolute structure parameter value (and s.u. value) obtained from any refinement with Friedel pairs, as justification of the merging of Friedel-pair data. Users of SHELXL-97 can merge Friedel-pair data with the MERG 3 instruction. |
IF Z < Si .and. radiation is MoKa .and. NFDRAT > 0.05 issue a General ALERT
"ALERT: MoKa measured Friedel data cannot be used to determine absolute
structure in a light-atom study EXCEPT under VERY special conditions."
| With non-centrosymmetric structures and Mo radiation, if no atoms heavier than Si are present, the DELTA-f'' terms in the scattering factor expression are very small. In such cases, if no useful absolute structure parameter can be refined (i.e. the value of the absolute structure parameter is meaningless because of its large s.u. value), authors should consider merging Friedel-pair reflections before final refinement, and stating this in the _publ_section_exptl_refinement section of the CIF, along with the meaningless absolute structure parameter value (and s.u. value) obtained from any refinement with Friedel pairs, as justification of the merging of Friedel-pair data. Users of SHELXL-97 can merge Friedel-pair data with the MERG 3 instruction. |
|
The ratio of reflections used in the refinement to refined parameters
(the r/p ratio) is important for ensuring precise atomic and
geometric parameters. Higher r/p ratios generally improve the precision.
It is expected that for centrosymmetric space groups, the r/p ratio should be at least 10:1. This also applies for non-centrosymmetric space groups when an element heavier than chlorine is present, because the heavy atom usually improves the diffracting power of the sample to an extent that makes it worthwhile to collect additional high angle data and thereby obtain higher r/p ratios. For non-centrosymmetric space groups when only elements lighter than argon are present, it is expected that the r/p ratio should be at least 8:1.
If you are having difficulty obtaining a suitable r/p ratio, consider
the following: Note that if you have measured data to at least sin(theta)/lambda of 0.6 (theta(max) = 25 deg. for Mo radiation; theta(max) = 67 deg. for Cu radiation) and you have used all available unique reflections in the refinement, the reflection/parameter test is not applied, because it is considered that you have measured an appropriate quantity of data and that you have made the best possible use of that data. Also note that with light atom non-centrosymmetric structures where anomalous dispersion effects are insignificant, it is unwise to attempt to use unmerged Friedel-related reflections simply to boost the r/p ratio. |
|
The value of _refine_ls_R_factor_gt is equivalent to the
conventional R-factor and when calculated using a threshold of
2sigma(I) in _reflns_threshold_expression, values less than 0.07
are normally expected. Higher values should be accompanied by
a suitable explanation in the _publ_section_exptl_refinement section.
However, authors should first ensure that there are not overlooked
problems associated with the data or the model. Elevated values for
_refine_ls_R_factor_gt may be indicative of a need to recollect the
data from a crystal of higher quality or to improve or correct the
model. Consider the following: (a) The absorption corrections are inadequate or inappropriate. (b) The overall quality of the data may be poor due to the crystal quality. (c) There is untreated twinning either in the form of unconsidered merohedral twinning or where overlap from the second twin domain in non-merohedral twins (which may have been ignored in the data collection) causes errors in the intensities of some reflections. (d) The model is incorrect or incomplete in terms of incorrect element assignment, missing atoms or unmodelled or inadequately modelled disorder or solvent atoms. |
| You are using an "old-fashioned", but still legal data name: _refine_ls_R_factor_obs. Please update the item to match the currently preferred name of _refine_ls_R_factor_gt. To ease this problem for the future, it is recommended that you upgrade or modify your CIF generating software accordingly. |
| It is compulsory to report the conventional R-factor under the item _refine_ls_R_factor_gt. This data name is not present in your CIF or has not been assigned a value. Please insert the data item with an apropriate value. |
|
The value of _refine_ls_wR_factor_ref should normally be considerably
less than 0.20. Higher values should be accompanied by
a suitable explanation in the _publ_section_exptl_refinement section.
However, authors should first ensure that there are not overlooked
problems associated with the data or the model. Elevated values for
_refine_ls_wR_factor_ref may be indicative of a need to recollect the
data from a crystal of higher quality or to improve or correct the
model. Consider the following: (a) The absorption corrections are inadequate or inappropriate. (b) The overall quality of the data may be poor due to the crystal quality. (c) The crystal is very weakly diffracting, so that a large proportion of essentially "unobserved" reflections are being used in the refinement. You should consider using a better crystal or a data collection at low temperature and/or, if the compound is organic, using Cu radiation. (d) There is untreated twinning either in the form of unconsidered merohedral twinning or where overlap from the second twin domain in non-merohedral twins (which may have been ignored in the data collection) causes errors in the intensities of some reflections. (e) The model is incorrect or incomplete in terms of incorrect element assignment, missing atoms or unmodelled or inadequately modelled disorder or solvent atoms. |
| You are using an "old-fashioned", but still legal data name: _refine_ls_wR_factor_obs. Please update the item to match the currently preferred name of _refine_ls_wR_factor_ref. To ease this problem for the future, it is recommended that you upgrade or modify your CIF generating software accordingly. |
| It is compulsory to report the weighted R-factor under the item _refine_ls_wR_factor_ref. This data name is not present in your CIF or has not been assigned a value. Please insert the data item with an appropriate value. |
|
The value of _diffrn_reflns_av_R_equivalents should normally be
considerably less than 0.10. Higher values should be accompanied by
a suitable explanation in the _publ_section_exptl_refinement section.
However, authors should first ensure that there are not overlooked
problems associated with the data or the space group. Elevated
values for _diffrn_reflns_av_R_equivalents may be indicative of a
need to recollect the data from a crystal of higher quality or that
there is a problem with the data treatment. Consider the following: (a) The absorption corrections are inadequate or inappropriate. (b) The overall quality of the data may be poor due to the crystal quality. (c) The crystal is very weakly diffracting, so that a large proportion of essentially "unobserved" reflections are being used in the refinement. You should consider using a better crystal or a data collection at low temperature and/or, if the compound is organic, using Cu radiation. (d) You are working in the wrong crystal system or Laue group. (e) You have only a very small number of equivalent reflections, which may lead to artificially high values of _diffrn_reflns_av_R_equivalents Note that if _diffrn_reflns_av_sigmaI/netI is also large, the quality of the data should be considered to be suspect. |
| An elevated value for the largest parameter shift/s.u. is indicative that proper convergence of the refinement has not yet been achieved. Additional cycles of refinement are usually sufficient to achieve adequate convergence and remove this alert. In disordered or otherwise poorly behaved structures, many additional cycles may be required before a suitable level of convergence has been achieved. Any parameters that remain constantly oscillating should be detailed in the _publ_section_exptl_refinement section. You should also consider whether appropriate restraints might help to stabilise ill-defined and oscillating parameters. |
| You are using an "old-fashioned", but still legal data name: _refine_ls_shift/esd_max. Please update the item to match the currently preferred name of refine_ls_shift/su_max. To ease this problem for the future, it is recommended that you upgrade or modify your CIF generating software accordingly. |
| It is compulsory to report the largest parameter shift/s.u. value in the final refinement cycle under the item _refine_ls_shift/su_max. This data name is not present in your CIF or has not been assigned a value. Please insert the data item with an appropriate value. |
|
You have entered a value for Flack's absolute structure parameter (or
the software has automatically entered one for you because you have a
non-centrosymmetric space group).
If the absolute structure parameter is meaningless because the compound is a weak anomalous scatterer (i.e. no atom heavier than Si is present), it is best to remove the absolute structure parameter from the CIF. If the absolute structure parameter is meaningful, then you have forgotten to 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).] |
|
You have entered a value for Rogers' absolute structure parameter (or
the software has automatically entered one for you because you have a
non-centrosymmetric space group).
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, then you have forgotten to 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).] Note that the use of Rogers' absolute structure parameter cannot cope with merohedral twins or cases where there is a partial mix of enantiomers. It is recommended that you refine using Flack's absolute structure parameter instead. |
|
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).] |
|
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).] |
| 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. |
|
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. |
| 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. |
|
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).] |
| 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. |
|
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).] |
|
The space group symbol given under _symmetry_space_group_name_H-M is
missing, or it cannot be recognised and/or does not correspond with
the space group number given under symmetry_space_group_number.
Note that this message usually means that you have incorrectly formatted the space group symbol. Do not insert subscript formatting or parentheses in the space group symbol. You must leave spaces between symbols referring to different axes. Examples for _symmetry_space_group_name_H-M:
Note that the H-M symbol does not necessarily contain complete information about the symmetry and the space-group origin. If used always supply the FULL symbol from International Tables for Crystallography, Vol. A (1992) and indicate the origin and the setting if it is not implicit. If there is any doubt that the equivalent positions can be uniquely deduced from this symbol specify the _symmetry_equiv_pos_as_xyz *_Hall data items as well. |
|
The space group symbol given under _symmetry_space_group_name_H-M
cannot be matched with the space group symmetry operators given under
_symmetry_equiv_pos_as_xyz.
Check that you have fully and correctly specified and formatted both _symmetry_space_group_name_H-M and _symmetry_equiv_pos_as_xyz and that they both refer to the SAME space group and the SAME setting of the axes. _symmetry_equiv_pos_as_xyz must include ALL symmetry operators for the space group concerned, including the identity x,y,z, all those related by a centre of inversion and all those related by a non-primitive lattice operation.
Example: The space group symbol must not include subscript formatting or parentheses. You must leave spaces between symbols referring to different axes. Examples for _symmetry_space_group_name_H-M:
Note that the H-M symbol does not necessarily contain complete information about the symmetry and the space-group origin. If used always supply the FULL symbol from International Tables for Crystallography, Vol. A (1992) and indicate the origin and the setting if it is not implicit. If there is any doubt that the equivalent positions can be uniquely deduced from this symbol specify the _symmetry_equiv_pos_as_xyz *_Hall data items as well. |
_symmetry_cell_setting must ONLY be one of the following keywords
(do not add extra text to this field - e.g. 'monoclinic C-centred'
or 'rhombohedral - hexagonal setting' are incorrect):
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The unit cell parameters do not seem to be consistent with the
expected constraints implied by the crystal system specified
under _symmetry_cell_setting. Check that the crystal system
has been correctly specified and that the unit cell parameters
have been constrained where necessary.
For example, a monoclinic unit cell should not be specified with an angle of 89.98 deg. for an angle that should be exactly 90 deg due to the symmetry requirements. Such unit cell parameters should be constrained to appropriate values during the unit cell refinement. Similarly, a tetragonal unit cell should have identical values for the lengths of the a and b axes. Of course, it is possible that two unit cell axes coincidentally have virtually equal lengths in a low symmetry crystal system or that a monoclinic structure has a beta angle that is indistinguishable from 90.0 deg. In such cases, these alerts can be ignored. |
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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:
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The Commission on Journals has determined that setting the maximum
sin(theta)/lambda for measurements to at least 0.6 is both optimal and
achievable for most structural studies. The extent of the data not
only affects the ratio of measurements to refined parameters and hence
the accuracy of the atomic and geometric parameters, but also
the reliability of the angular dependent terms, such as Uijs.
It is unlikely that any submitted CIF which contains the results of a data collection with a lower theta(max) will be accepted for publication unless there are exceptional circumstances. Old data claimed to have been collected when less stringent criteria were in place will not be excepted. You should routinely set your diffractometer so that a theta(max) of 25 deg. for Mo radiation or 67 deg. for Cu radiation is the minimum that is achieved. If the crystal diffracts sufficiently well, it is strongly recommended that theta(max) is set to an even higher value. It is understood that there may be little point in collecting background "noise" when a weakly diffracting crystal gives no detectable diffraction above theta values well below our required limit. In such a case, you should first ensure that you have conscientiously undertaken all possible steps to ensure that the experiment has been able to extract the best diffracting power from your sample. To this end, all of the following options should have been exhausted: (a) The best possible crystal has been sought and utilised for the data collection. If the crystal was small or of poor quality, are you sure that a better or bigger one cannot be obtained? The chosen crystal may have been the best one in the batch, but had enough effort and patience really been expended in the crystallisation attempt? Often, lack of experience, impatience or unwillingness to try another crystallisation technique or solvent leads to the experimentalist abandoning crystallisation attempts before the optimal conditions have been found. Before you blame the crystal quality, be sure that you have convinced yourself that nothing further can be done in this direction. (b) Use low temperature measurements to enhance the reflection intensities and the extent of the "observed" data. (c) For organic compounds, try data collection with Cu radiation, which significantly enhances the reflection intensities. |
_refine_ls_weighting_scheme must be included in the CIF. Use
one of the following keywords (do not add extra text to this
field - e.g. including the weighting equation is not correct):
The equation for the weighting scheme must be given under _refine_ls_weighting_details.
Example: |
_refine_ls_weighting_scheme must be included in the CIF. Use
one of the following keywords (do not add extra text to this
field - e.g. including the weighting equation is not correct):
Example: Note that although unit weights are allowed for in the CIF dictionary, structures refined with unit weights are not acceptable. |
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