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Re: Approval of CIF core changes for 2.3
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- Subject: Re: Approval of CIF core changes for 2.3
- From: Howard Flack <[email protected]>
- Date: Tue, 8 Jul 2003 11:04:50 +0100 (BST)
Part 1 of comments from HDF.
> # _cell_formula_units_Z
HDF # _cell_formula_units_Z_prime
># CHEMICAL
># _chemical_melting_point_gt
HDF Isn't _chemical_melting_point itself missing here since it is
supposed to be changed to get _type_conditions esd
> # _diffrn_reflns_measured_faction_resolution_full
> # _diffrn_reflns_measured_faction_resolution_max
HDF # _diffrn_reflns_measured_fraction_resolution_full
HDF # _diffrn_reflns_measured_fraction_resolution_max
># _Space_group_crystal_system
># _Space_group_id (Parent to various .sg_id's)
># _Space_group_IT_number
># _Space_group_name_Hall
># _Space_group_name_H-M_alt
HDF All Space should be space
>data_atom_site_refinement_flags_posn
> _name '_atom_site_refinement_flags_posn'
> _category atom_site
> _type char
> _list yes
> _list_reference '_atom_site_label'
> loop_ _enumeration
> _enumeration_detail . 'no refinement constraints'
HDF _enumeration_detail . 'no constraints on positional
coordinates'
> D 'distance or angle restraint on site'
HDF D 'distance or angle restraint on
positional coordinates'
> G 'rigid group refinement of site'
HDF G 'rigid group refinement of positional
coordinates'
> R 'riding-atom site attached to non-riding atom'
> S 'special position constraint on site'
HDF S 'special position constraint on
positional coordinates'
> DG 'combination of the above constraints'
>data_atom_site_refinement_flags_adp
> _name '_atom_site_refinement_flags_adp'
> _category atom_site
> _type char
> _list yes
> _list_reference '_atom_site_label'
> loop_ _enumeration
> _enumeration_detail . 'no refinement constraints'
HDF _enumeration_detail . 'no constraints on atomic
displacement parameters'
> T 'atomic displacement constraints'
HDF T 'special-position constraints on
atomic displacement parameters'
> U 'Uiso or Uij restraint (rigid bond)'
> TU 'Both constraints applied'
> _definition
>; A code which indicates the refinement restraints or constraints
> applied to this atomic displacement parameters of this site.
HDF applied to the atomic displacement parameters of this
site.
>;
>;
># COMMENT: Are these enumeration details clear?
HDF I think mine are better than yours!
> What is the difference
># between these two flags? Can both apply at the same time?
HDF Yes. If I had to choose I would not have chosen T and U as the
characters.
># STATUS: Preliminary approval 02-09-23
>data_atom_site_refinement_flags_occupancy
> _name '_atom_site_refinement_flags_occupancy'
> _category atom_site
> _type char
> _list yes
> _list_reference '_atom_site_label'
> loop_ _enumeration
> _enumeration_detail . 'no refinement constraints'
HDF _enumeration_detail . 'no constraints on site occupancy
parameters'
> P 'partial occupancy constraint'
HDF P 'site occupancy constraint'
_definition
; A code which indicates that refinement restraints or
constraints were applied to the occupancy of this site.
;
# STATUS: Preliminary approval 02-09-23
>data_cell_formula_units_Z_prime
> _name '_cell_formula_units_Z_prime'
> _category cell
> _type numb
> _enumeration_range 1:
> _definition
>; The number of the formula units as specified
> by _chemical_formula_structural, _chemical_formula_moiety or
> _chemical_formula_sum in the asymmetric unit of the
> unit cell given in the CELL category and the
> space group defined in the SYMMETRY or SPACE GROUP category.
> This item is used to indicate the number of chemically
> equivalent molecules in the asymmetric unit.
>;
># COMMENT: Requested by CCDC
># STATUS: Preliminary approval 2002-10-14
HDF. *********
There are two HUGE problems with this definition. I recommend you send
it back to the CCDC for more careful consideration.
(1) There is not in fact a single Z' which describes what they are
trying to express. Take the example of the compound AB composed of two
molecules A and B in the ratio 1:1 as represented by the chemical
formula AB. The structure is in space group P2. Molecules A have point
symmetry 2 and sit on a 2-fold axis in the crystal structure. There are
two independent A molecules in the asymmetric unit. Molecules B have
symmetry 1 and sit in a general position. There is one independent
molecule B in the asymmetric unit. What is the value of your Z'?
(2) And, surprise surprise coming from HDF, there are problems of
chirality with this Z'.
_chemical_formula_structural
_chemical_formula_moiety
_chemical_formula_sum and
chemically equivalent molecules
do not necessarily refer to the same thing. Some may group opposite
enantiomers together and other may separate them. Opposite enantiomers
are not (in my view) "chemically equivalent molecules". In J. Appl.
Cryst. 33, 1143-1148, F&B (2000) wrote in section 3.10 on Molecular
symmetry "For this purpose, the most promising nomenclature suggested so
far is that of Chernikova et al (1991), but this would need to be
extended for the current purposes." CCDC has made a big step in the
right direction with their 'CSD symmetry' but this does not capture
chirality information. No one has tried to work out the way that
Chernikova's nomenclature could be usefully extended for encoding
molecular symmetry and chirality information. This is what is really
required and it needs to be provided by authors at publication time. A
single vague Z' is of limited practical value.
Back to the drawing board. (When the daffodils come into bloom next
spring, it would be a good time to have a small punting party working on
this problem!)
end of HDF ********
>data_cell_reciprocal_length_
> loop_ _name '_cell_recirpocal_length_a'
HDF loop_ _name '_cell_reciprocal_length_a'
> '_cell_reciprocal_length_b'
> '_cell_reciprocal_length_c'
># CHANGE TO AN EXISTING ITEM
>#
># _chemical_melting_point should have added:
>#
># _type_conditions esd
>#
HDF It is not clear to me whether you have applied the above correction
or not.
>data_chemical_melting_point_
> loop_ _name '_chemical_melting_point_gt'
> '_chemical_melting_point_lt'
> _category chemical
> _type numb
> _related_item '_chemical_melting_point'
> _related_function alternate
> _enumeration_range 0.0:
> _units K
> _units_detail 'Kelvins'
> _definition
>; A temperature in Kelvins which represents an upper
> limit (_*_lt) or a lower limit (_*_gt) to the melting point,
> the temperature at which a
> crystalline solid changes to a liquid. These items allow a
HDF; A temperature in Kelvins below which
HDF (_*_lt) or above which (_*_gt) the melting point,
HDF the temperature at which a
HDF crystalline solid changes to a liquid, lies. These
items allow a
> range of temperatures to be
> given. _chemical_melting_point should always be
> used in preference to these items whenever possible.
>;
># COMMENT: These item are introduced to allow for a maximum or minimum
># limit, or a range of temperatures to be given. They are primarily designed
> # to allow comments in exiting databases to be included in a CIF.
HDF # to allow comments in existing databases to be included in a CIF.
HDF **** I'm not sure that the way you are saying things is good
thermodynamics. The melting temperature is the equilibrium temperature
between a solid and a liquid phase. The composition of both the solid
phase and the liquid phase is crucial to determining this temperature.
If there is any smack of a mixture around your definition has
difficulties. For a sample of fixed composition, the lowest temperature
of liquid formation on raising the temperature of the solid phase, is
not the same as the highest temperature of solid formation on lowering
the temperature of the liquid phase.
end of HDF ****
># STATUS: Preliminary approval 2002-10-14
> data_chemical_temperature_decomposition
> data_chemical_temperature_decomposition_*
> data_chemical_temperature_sublimation
> data_chemical_temperature_sublimation_*
HDF How about an enumeration range for these?
>data_chemical_temperature_decomposition_*
> loop_ _name '_chemical_temperature_decomposition_gt'
> '_chemical_temperature_decomposition_lt'
> _category chemical
> _type numb
> _units K
> _units_detail Kelvin
> _related_item '_chemical_temperature_decomposition'
> _related_function alternate
> _example 350
> _definition
>; A temperature below which (_*_lt) or above which (_*_gt) the
> solid is known to decompose, These items allow a range of
HDF solid is known to decompose. These items allow a range
of
> temperatures to be given.
> _chemical_temperature_decomposition should always be used in
> preference to these items whenever possible.
> loop_ _name '_chemical_temperature_sublimation_gt'
> '_chemical_temperature_sublimation_lt'
> _category chemical
> _type numb
> _units K
> _units_detail Kelvin
> _related_item '_chemical_temperature_sublimation'
> _related_function Alternate
> _example 350
> _definition
> ; A temperature below which (_*_lt) of above which (_*_gt) the
HDF; A temperature below which (_*_lt) or above which
(_*_gt) the
> solid is known to sublime,
HDF solid is known to sublime.
> These items allow as range of temperatures to be given.
HDF These items allow a range of temperatures to be given.
> _chemical_temperature_sublimation should always be used in
> preference to these items whenever possible.
;
>data_diffrn_ambient_pressure_
> loop_ _name
> '_diffrn_ambient_pressure_gt'
> '_diffrn_ambient_pressure_lt'
> _category diffrn
> _type numb
> _type_conditions esd
> _related_item '_diffrn_ambient_pressure'
> _related_function alternate
> _enumeration_range 0.0:
> _units kPa
> _units_detail 'kilopascals'
> _definition
> ; The mean pressure in kilopascals above which (_*_gt) or below
HDF; The mean hydrostatic pressure in kilopascals above
which (_*_gt) or below
> which (_*_lt) the intensities were measured. These items allow
> for a pressure range to be given. _diffrn_ambient_pressure
> should always be used in preference to these items whenever
> possible.
;
# COMMENT; Provides for a pressure range to be indicated.
# STATUS: Preliminary approval 2002-11-11
>data_diffrn_standards_decay_%_lt
> _name '_diffrn_standards_decay_%_lt'
> _category diffrn_standards
> _type numb
> _related_item '_diffrn_standards_decay_%'
> _related_function alternate
> _enumeration_range :100
> _definition
>; An upper limit on the percentage decrease in the mean
> intensity of the set of standard reflections measured at the
> start of the measurement of the diffraction pattern and at the
> end. This value is used when the decay is too small to be
> detected.
>;
># COMMENT: Many experiments show no detectable decay and there is no provision
># for this at the moment other than to enter 0.0.
HDF And what pray is wrong with entering 0.0 with its standard
uncertainty?
H.
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