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Re: Approval requested for CIF Core 2.1
- To: Multiple recipients of list <coredmg@iucr.org>
- Subject: Re: Approval requested for CIF Core 2.1
- From: Brian McMahon <bm@iucr.org>
- Date: Mon, 8 Feb 1999 16:49:21 GMT
I am very grateful indeed to everyone who reviewed and discussed the version
2.1beta5 of the core dictionary that I posted just before Christmas. I have
implemented your recommendations as best I understand them, and I attach to
this message a difference listing between the version I sent out in December
and the current working version.
There is one more task I wish to do before formally submitting this version
to COMCIFS. Syd has requested a couple of structural modifications, one of
which I am happy to implement at this time. That is the use of a separate
data block for *each* definition. Currently some data blocks hold several
definitions, e.g.
data_exptl_absorpt_correction_T_
loop_ _name '_exptl_absorpt_correction_T_max'
'_exptl_absorpt_correction_T_min'
The proposal would be to split this into two data blocks:
data_exptl_absorpt_correction_T_ max
_name '_exptl_absorpt_correction_T_max'
data_exptl_absorpt_correction_T_ min
_name '_exptl_absorpt_correction_T_min'
The use of a single data block for multiple definitions had two functions
originally - one was the convenient collecting together of data items that
had a similar function and could be described by the same attributes and
umbrella definition; the other was to collect items that together formed an
irreducible data unit. For example,
data_refln_index_
loop_ _name '_refln_index_h'
'_refln_index_k'
'_refln_index_l'
_category refln
indicates that h,k,l together form a meaningful unit. In mmCIF and other
DDL2 dictionaries, every data name is defined in a separate save frame (here
fulfilling the same role as the DDL1 data blocks), but data items related in
the way of the h,k,l Miller indices are given the same value of
"_item_sub_category.id"
I am entirely happy about separating off the data names that are simply
collected together for convenience; I am a little more hesitant about
doing so for those intimately linked like the Miller indexes examples,
but would raise no objections on the understanding that a new DDL1 term
could be introduced to make this relationship specific if it is thought
really necessary.
Other opinions on this will be welcome. If there is any dissension or strong
reservations I shall drop this proposed rearrangement from this revision,
and instead raise the topic for discussion in the COMCIFS list.
Best wishes
Brian
==============================================================================
Differences between current working version (prefixed '<') and version
2.1beta5 of December 1998 (prefixed '>'):
19c19
< _dictionary_update 1999-02-06
---
> _dictionary_update 1998-12-15
330,376d329
< 1999-01-16 BMcM: coreDMG review of version 2.1beta5. Numerous small changes
< from I.D.Brown, the most significant being:
< _atom_site_occupancy definition clarifies how to impose an
< experimental uncertainty on the _enumeration_range;
< _atom_site_U_iso_or_equiv enumeration range set to infinity;
< _atom_type_analytical_mass_% enumeration range set as 0:100;
< expanded definitions of _diffrn_radiation_probe and *_type to
< clarify the distinction between these two items;
< added reference to _exptl_crystal_size to the definition of
< _exptl_crystal_description, and modified the definition of
< _exptl_crystal_face_diffr_ ;
< new data item _refln_d_spacing;
< clarified the role of _reflns_special_details in specifying
< whether Friedel pairs have been averaged;
< Numerous small changes from H.D.Flack, most significantly:
< removed enumeration range from _diffrn_reflns_counts_ because
< *_net can go negative;
< fixed various typos in equations for wR and S;
< removed reference to Friedel reflections from
< _refln_symmetry_multiplicity
< 1999-01-24 BMcM: further revision to wording of _refln_symmetry_multiplicity
< following discussions by HDF and IDB
< Numerous small changes from G.Madariaga, most significantly:
< a instead of A for real-space cell lengths
< (_atom_site_B_iso_or_equiv and _atom_site_U_iso_or_equiv);
< _related_function alternate for _atom_site_Cartn_ & _fract_;
< "or scattering lengths" added to _atom_type_scat_source;
< deleted incorrect _list_reference in DIFFRN_RADIATION;
< added rtf to enumeration in _publ_body_format;
< added enumeration range to _refine_ls_abs_structure_Rogers
< 1999-02-04 BMcM: fixed some long lines
< 1999-02-06 BMcM: data names using sigma as an indicator of experimental
< standard uncertainty replaced by equivalents using the
< preferred 'u' notation (HDF):
< _diffrn_refln_intensity_sigma
< _diffrn_reflns_av_sigmaI/netI
< _diffrn_reflns_class_av_sgI/I
< _diffrn_standards_scale_sigma
< _reflns_shell_meanI_over_sigI_all
< _reflns_shell_meanI_over_sigI_gt
< (_reflns_shell_meanI_over_sigI_obs already replaced by *_gt)
< addition of '_related function alternate' to new data
< items corresponding to old items with
< '_related_function replace' (SRH)
< Example for _citation_journal_id_CSD changed to 0070 to
< reflect current practice at PDB (F.C.Bernstein)
< Added _atom_type_scat_dispersion_source (GM)
464d416
<
498,499d449
< _related_item '_atom_site_thermal_displace_type'
< _related_function alternate
681c631
< B(equiv) = (1/3) sum~i~[sum~j~(B^ij^ a*~i~ a*~j~ a~i~ a~j~)]
---
> B(equiv) = (1/3) sum~i~[sum~j~(B^ij^ a*~i~ a*~j~ A~i~.A~j~)]
683c633
< a = the real-space cell lengths
---
> A = the real-space cell lengths
720,723c670,673
< ; A standard code to signal if the site coordinates have been
< determined from the intensities or calculated from the geometry
< of surrounding sites, or have been assigned dummy coordinates.
< The abbreviation 'c' may be used in place of 'calc'.
---
> ; A standard code to signal if the site data have been determined
> from the intensities or calculated from the geometry of
> surrounding sites, or have been assigned dummy coordinates. The
> abbreviation 'c' may be used in place of 'calc'.
733,734d682
< _related_item '_atom_site_fract_'
< _related_function alternate
831,832d778
< _related_item '_atom_site_Cartn_'
< _related_function alternate
924,927c870
< may not significantly exceed 1.0 unless it is a dummy site. The
< value must lie in the 99.97% Gaussian confidence interval
< -3u =< x =< 1 + 3u. The _enumeration_range of 0.0:1.0 is thus
< correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u).
---
> may not significantly exceed 1.0 unless it is a dummy site.
1043c986
< _enumeration_range 0.0:
---
> _enumeration_range 0.0:10.0
1054c997
< U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~ a~j~)]
---
> U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ A~i~.A~j~)]
1056c999
< a = the real-space cell lengths
---
> A = the real-space cell lengths
1265c1208
< _enumeration_range 0.0:100
---
> _enumeration_range 0.0:
1338c1281,1282
< the scattering factors for this atom type.
---
> the scattering factors for this atom type. May be entered in any
> order.
1360,1371d1303
< data_atom_type_scat_dispersion_source
< _name '_atom_type_scat_dispersion_source'
< _category atom_type
< _type char
< _list yes
< _list_reference '_atom_type_symbol'
< _example 'International Tables Vol. IV Table 2.3.1'
< _definition
< ; Reference to source of real and imaginary dispersion
< corrections for scattering factors used for this atom type.
< ;
<
1392,1393c1324,1325
< _list_reference '_atom_type_symbol'
< _example 'International Tables Vol. IV Table 2.4.6B'
---
> _list_reference '_atom_type_symbol'
> _example 'International Tables Vol. IV Table 2.4.6B'
1395,1396c1327,1328
< ; Reference to source of scattering factors or scattering lengths
< used for this atom type.
---
> ; Reference to source of scattering factors used for this atom
> type.
2060c1992
< only for diffractometer measurements.
---
> only for diffractometer data.
2416a2349,2350
> Within an _atom_site_ list this number must match with one of
> the _atom_site_chemical_conn_number values.
2659c2593
< and atom site lists should not be included in this formula (see
---
> and atom site data should not be included in this formula (see
2933c2867
< _example '0070'
---
> _example '070'
2937c2871
< system used at the Protein Data Bank (PDB).
---
> system used at the Brookhaven Protein Data Bank (PDB).
3146a3081
> _list_link_parent '_citation_id'
3218a3154
> _list_link_parent '_citation_id'
3311d3246
< '_database_code_PDB'
3319,3320c3254,3255
< NBS (NIST) Crystal Data Database (lattice parameters); Protein
< data Bank, and the Powder Diffraction File (JCPDS/ICDD).
---
> NBS (NIST) Crystal Data Database (lattice parameters) and the
> Powder Diffraction File (JCPDS/ICDD).
3547a3483,3490
> data_diffrn_detector_details
> _name '_diffrn_detector_details'
> _category diffrn_detector
> _type char
> _definition
> ; A description of special aspects of the radiation detector.
> ;
>
3552,3553d3494
< _related_item '_diffrn_radiation_detector'
< _related_function alternate
3574,3581d3514
< data_diffrn_detector_details
< _name '_diffrn_detector_details'
< _category diffrn_detector
< _type char
< _definition
< ; A description of special aspects of the radiation detector.
< ;
<
3585,3586d3517
< _related_item '_diffrn_radiation_detector_dtime'
< _related_function alternate
3889a3821,3822
> _list both
> _list_reference '_diffrn_radiation_wavelength_id'
3900a3834,3835
> _list both
> _list_reference '_diffrn_radiation_wavelength_id'
3911a3847,3848
> _list both
> _list_reference '_diffrn_radiation_wavelength_id'
3921a3859,3860
> _list both
> _list_reference '_diffrn_radiation_wavelength_id'
3933a3873,3874
> _list both
> _list_reference '_diffrn_radiation_wavelength_id'
3946a3888,3889
> _list both
> _list_reference '_diffrn_radiation_wavelength_id'
3960a3904,3905
> _list both
> _list_reference '_diffrn_radiation_wavelength_id'
3966,3969c3911,3913
< ; The nature of the radiation used (i.e. name of subatomic particle
< or region of the electromagnetic spectrum). It is strongly
< encouraged that this field be specified so that the probe
< radiation can be simply determined.
---
> ; Name of the type of radiation used. It is strongly encouraged
> that this field be specified so that the probe radiation
> can be simply determined.
3975a3920,3921
> _list both
> _list_reference '_diffrn_radiation_wavelength_id'
3979,3982c3925,3926
< ; The type of the radiation. This represents a finer-grained
< level of description than _diffrn_radiation_probe and is
< typically a description of the X-ray wavelength in Siegbahn
< notation.
---
> ; The nature of the radiation. This is typically a description
> of the X-ray wavelength in Siegbahn notation.
3988a3933,3934
> _list both
> _list_reference '_diffrn_radiation_wavelength_id'
4122c4068
< (The DIFFRN_REFLNS data items specify the parameters that apply
---
> The DIFFRN_REFLNS data items specify the parameters that apply
4124c4070
< are not looped.)
---
> are not looped.
4172,4173c4118,4119
< that, in addition to h,k,l, index the corresponding diffraction
< vector in the basis defined for the reciprocal lattice.
---
> that, in addition to h,k,l, index the corresponding
> diffraction vector in the basis defined for the reciprocal cell.
4185a4132
> _enumeration_range 0:
4250,4251c4197,4199
< data_diffrn_refln_intensity_net
< _name '_diffrn_refln_intensity_net'
---
> data_diffrn_refln_intensity_
> loop_ _name '_diffrn_refln_intensity_net'
> '_diffrn_refln_intensity_sigma'
4258,4259c4206,4208
< ; Net intensity calculated from the diffraction counts after
< the attenuator and standard scales have been applied.
---
> ; Net intensity and standard uncertainty (e.s.d.) calculated from
> the diffraction counts after the attenuator and standard scales
> have been applied.
4262,4291d4210
< data_diffrn_refln_intensity_sigma
< _name '_diffrn_refln_intensity_sigma'
< _category diffrn_refln
< _type numb
< _related_item '_diffrn_refln_intensity_u'
< _related_function replace
< _list yes
< _list_reference '_diffrn_refln_index_'
< _enumeration_range 0:
< _definition
< ; Standard uncertainty (e.s.d.) of the net intensity calculated
< from the diffraction counts after the attenuator and standard
< scales have been applied.
< ;
<
< data_diffrn_refln_intensity_u
< _name '_diffrn_refln_intensity_u'
< _category diffrn_refln
< _type numb
< _related_item '_diffrn_refln_intensity_sigma'
< _related_function alternate
< _list yes
< _list_reference '_diffrn_refln_index_'
< _enumeration_range 0:
< _definition
< ; Standard uncertainty of the net intensity calculated from
< the diffraction counts after the attenuator and standard
< scales have been applied.
< ;
<
4339d4257
< _enumeration_range 0.0:
4353d4270
< _enumeration_range 0.0:
4397,4398c4314,4315
< ; A code identifying that this reflection was measured as a
< standard intensity. The value must be '.' or match one of
---
> ; The code identifying that this reflection was measured as a
> standard intensity. This is the case if the code matched one of
4414c4331
< for reflections measured using energy dispersive detectors or the
---
> for data collected using energy dispersive detectors or the
4445c4362
< _diffrn_reflns_av_unetI/netI .027
---
> _diffrn_reflns_av_sigmaI/netI .027
4463a4381,4383
> The DIFFRN_REFLN data items refer to individual intensity
> measurements, and must be included in looped lists.
>
4467,4469d4386
<
< (The DIFFRN_REFLN data items refer to individual intensity
< measurements, and must be included in looped lists.)
4478,4481c4395,4397
< ; The residual [sum av|del(I)| / sum |av(I)|] for
< symmetry-equivalent reflections used to calculate the
< average intensity av(I). The av|del(I)| term is the
< average absolute difference between av(I) and the
---
> ; The residual [sum|avdel(I)| / sum|av(I)|] for symmetry-equivalent
> reflections used to calculate the average intensity av(I). The
> avdel(I) term is the average difference between av(I) and the
4489,4490d4404
< _related_item '_diffrn_reflns_av_unetI/netI'
< _related_function replace
4493c4407
< ; Measure [sum u(net I)|/sum|net I|] for all measured reflections.
---
> ; Measure [sum|sigma(I)|/sum|net(I)|] for all measured reflections.
4496,4506d4409
< data_diffrn_reflns_av_unetI/netI
< _name '_diffrn_reflns_av_unetI/netI'
< _category diffrn_reflns
< _type numb
< _related_item '_diffrn_reflns_av_sigmaI/netI'
< _related_function alternate
< _enumeration_range 0.0:
< _definition
< ; Measure [sum u(net I)|/sum|net I|] for all measured reflections.
< ;
<
4538c4441
< ; A description of the process used to reduce the intensities
---
> ; A description of the process used to reduce the intensity data
4550,4552c4453,4455
< ; The theta angle (in degrees) at which the measured reflection
< count is close to complete. The fraction of unique reflections
< measured out to this angle is given by
---
> ; The diffractometer theta angle (in degrees) at which the
> measured reflection count is close to complete. The fraction
> of unique reflections measured out to this angle is given by
4626c4529
< the reciprocal lattice.
---
> the reciprocal cell.
4644,4647c4547,4550
< [sum av|del(I)|/sum|av(I)|] for symmetry-equivalent reflections
< used to calculate the average intensity av(I). The av|del(I)|
< term is the average absolute difference between av(I) and the
< individual intensities.
---
> [sum|avdel(I)|/sum|av(I)|] for symmetry-equivalent reflections
> used to calculate the average intensity av(I). The avdel(I) term
> is the average difference between av(I) and the individual
> intensities.
4654,4655d4556
< _related_item '_diffrn_reflns_class_av_uI/I'
< _related_function replace
4660c4561
< ; Measure [sum|u(net I)|/sum|net I|] for all measured intensities
---
> ; Measure [sum|sigma(I)|/sum|net(I)|] for all measured intensities
4664,4677d4564
< data_diffrn_reflns_class_av_uI/I
< _name '_diffrn_reflns_class_av_uI/I'
< _category diffrn_reflns_class
< _type numb
< _related_item '_diffrn_reflns_class_av_sgI/I'
< _related_function alternate
< _list yes
< _list_reference '_diffrn_reflns_class_code'
< _enumeration_range 0.0:
< _definition
< ; Measure [sum|u(net I)|/sum|net I|] for all measured intensities
< in a reflection class.
< ;
<
4716c4603
< This is the smallest d value for this reflection class.
---
> This is the smallest d value for each reflection class.
4743c4630
< class, excluding the systematic absences arising from
---
> class, excluding the systematic extinctions arising from
4848,4849d4734
< _related_item '_diffrn_radiation_source'
< _related_function alternate
4864,4865c4749
< _type numb
< _enumeration_range 0.0:
---
> _type char
4885d4768
< _enumeration_range 0.0:
4936,4937c4819
< _type numb
< _enumeration_range 0.0:
---
> _type char
5075,5076d4956
< _related_item '_diffrn_standards_scale_u'
< _related_function replace
5083,5094d4962
< data_diffrn_standards_scale_u
< _name '_diffrn_standards_scale_u'
< _category diffrn_standards
< _type numb
< _related_item '_diffrn_standards_scale_sigma'
< _related_function alternate
< _enumeration_range 0.0:
< _definition
< ; The standard uncertainty of the individual mean
< standard scales applied to the intensity data.
< ;
<
5314,5317c5182,5183
< The crystal dimensions should not normally be reported here;
< use instead _exptl_crystal_size_ for the gross dimensions of
< the crystal, and _exptl_crystal_face_ to describe the
< relationship between individual faces.
---
> Dimensional data are better placed in the _exptl_crystal_face_
> data items.
5346,5347c5212
< loop_ _list_link_child '_diffrn_refln_crystal_id'
< '_refln_crystal_id'
---
> _list_link_child '_diffrn_refln_crystal_id'
5370,5371d5234
< _list both
< _list_reference '_exptl_crystal_id'
5403,5404d5265
< _list both
< _list_reference '_exptl_crystal_id'
5459,5463c5320,5321
< ; The goniometer angle settings in degrees when the perpendicular
< to the specified crystal face is aligned along a specified
< direction (e.g. the bisector of the incident and reflected beams
< in an optical goniometer).
<
---
> ; The diffractometer angle settings in degrees for a specific
> crystal face associated with _exptl_crystal_face_perp_dist.
6564,6566c6422,6424
< and _publ_section_exptl_solution items are preferred for
< separating the chemical preparation, refinement and structure
< solution aspects of the experimental description.
---
> and _publ_section_exptl_solution items are preferred for separating
> the chemical preparation, refinement and structure solution
> aspects of the experimental description.
6765d6622
< rtf 'Rich Text Format'
6876c6733,6734
< in a journal request list is a standard CIF definition or not.
---
> in a journal request list is a standard CIF definition or not
> (flags are 'yes' or 'no').
6969,6970c6827,6828
< electrons per angstrom cubed, of the final difference electron
< density. The *_rms value is measured with
---
> electrons per angstrom cubed, of the electron density in the
> final difference Fourier map. The *_rms value is measured with
6983a6842
> For example, it may describe the Friedel pairs used.
7012d6870
< _enumeration_range -1.0:1.0
7016,7020d6873
< The value must lie in the 99.97% Gaussian confidence interval
< -3u =< \h =< 1 + 3u and a standard uncertainty (e.s.d.) u must
< be supplied. The _enumeration_range of -1.0:1.0 is correctly
< interpreted as meaning (-1.0 - 3u) =< \h =< (1.0 + 3u).
<
7139c6992
< { sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
---
> { sum | w | Y(obs) - Y(calc) |^2^ | }^1/2^
7162,7163d7014
< _related_item '_refine_ls_goodness_of_fit_obs'
< _related_function alternate
7173c7024
< { sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
---
> { sum | w | Y(obs) - Y(calc) |^2^ | }^1/2^
7206c7057
< { sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
---
> { sum | w | Y(obs) - Y(calc) |^2^ | }^1/2^
7368,7369d7218
< _related_item '_refine_ls_R_factor_obs'
< _related_function alternate
7421,7424c7270,7273
< ; Residual factor R(Fsqd), calculated on the squared amplitudes
< of the observed and calculated structure factors, for
< significantly intense reflections (satisfying
< _reflns_threshold_expression) and included in the refinement.
---
> ; Residual factor R(Fsqd), calculated on the squares of the
> observed and calculated structure factors, for all reflections
> flagged as observed (see _reflns_observed_criterion) and
> included in the refinement.
7437c7286
< and the sum is taken over the specified reflections
---
> sum is taken over the specified reflections
7446,7448c7295,7296
< ; Residual factor R(I) for significantly intense reflections
< (satisfying _reflns_threshold_expression) and included in
< the refinement.
---
> ; Residual factor R(I) for all reflections flagged as observed
> (see _reflns_observed_criterion) and included in the refinement.
7460c7308
< and the sum is taken over the specified reflections
---
> sum is taken over the specified reflections
7475,7476c7323,7324
< {sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
< { + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } }
---
> {sum | w | Y(obs) - Y(calc) |^2^ | )^1/2^
> ( + sum~r~ | w~r~ | P(calc) - P(targ) |^2^ | }
7506,7507d7353
< _related_item '_refine_ls_restrained_S_obs'
< _related_function alternate
7517,7518c7363,7364
< {sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
< { + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } }
---
> {sum | w | Y(obs) - Y(calc) |^2^ | )^1/2^
> ( + sum~r~ | w~r~ | P(calc) - P(targ) |^2^ | }
7558,7559c7404,7405
< {sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
< { + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } }
---
> {sum | w | Y(obs) - Y(calc) |^2^ | )^1/2^
> ( + sum~r~ | w~r~ | P(calc) - P(targ) |^2^ | }
7615,7616d7460
< _related_item '_refine_ls_shift/esd_max'
< _related_function alternate
7627,7628d7470
< _related_item '_refine_ls_shift/esd_mean'
< _related_function alternate
7695c7537
< ( sum w Y(obs)^2^ )
---
> ( sum w Y(calc)^2^ )
7710,7711d7551
< _related_item '_refine_ls_wR_factor_obs'
< _related_function alternate
7723c7563
< ( sum w Y(obs)^2^ )
---
> ( sum w Y(calc)^2^ )
7751c7591
< ( sum w Y(obs)^2^ )
---
> ( sum w Y(calc)^2^ )
7776c7616
< ( sum w Y(obs)^2^ )
---
> ( sum w Y(calc)^2^ )
7833c7673
< _list_link_parent '_reflns_class_code'
---
> _list_link_parent '_diffrn_reflns_class_code'
7839c7679
< match a _reflns_class_code.
---
> match a _diffrn_reflns_class_code.
7887,7895c7727,7730
<
< sum | F(obs) - F(calc) |
< R = ------------------------
< sum | F(obs) |
<
< F(obs) = the observed structure-factor amplitudes
< F(calc) = the calculated structure-factor amplitudes
<
< and the sum is taken over the reflections of this class. See also
---
> R=sum|F(obs)-F(calc)|/sum|F(obs)|
> F(obs)=the observed structure-factor amplitudes, F(calc)=the
> calculated structure-factor amplitudes, and the sum is taken over
> the specified reflections. See also
7908,7924c7743,7752
< on the squared amplitudes of the observed and calculated
< structure factors, for the reflections judged significantly
< intense (i.e. satisfying the threshold specified by
< _reflns_threshold_expression) and included in the refinement.
<
< The reflections also satisfy the resolution limits established
< by _refine_ls_class_d_res_high and _refine_ls_class_d_res_low.
<
< sum | F(obs)^2^ - F(calc)^2^ |
< R(Fsqd) = -------------------------------
< sum F(obs)^2^
<
< F(obs)^2^ = squares of the observed structure-factor amplitudes
< F(calc)^2^ = squares of the calculated structure-factor
< amplitudes
<
< and the sum is taken over the reflections of this class.
---
> on the squares of the observed and calculated structure factors,
> for the reflections judged significantly intense (i.e. satisfying
> the threshold specified by _reflns_threshold_expression) and
> included in the refinement. The reflections also satisfy the
> resolution limits established by _refine_ls_class_d_res_high and
> _refine_ls_class_d_res_low.
> R(F^2^)=sum|F(obs)^2^-F(calc)^2^|/sum|F(obs)^2^|
> F(obs)^2^=squares of the observed structure-factor amplitudes,
> F(calc)^2^=squares of the calculated structure-factor amplitudes,
> and the sum is taken over the specified reflections.
7942,7950c7770,7772
<
< sum | I(obs) - I(calc) |
< R(I) = ------------------------
< sum | I(obs) |
<
< I(obs) = the net observed intensities
< I(calc) = the net calculated intensities
<
< and the sum is taken over the reflections of this class.
---
> R(I)=sum|I(obs)-I(calc)|/sum|I(obs)|
> I(obs)=the net observed intensities, I(calc)=the net calculated
> intensities, and the sum is taken over the specified reflections
7965,7977c7787,7792
<
< ( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
< wR = ( ------------------------------ )
< ( sum w Y(obs)^2^ )
<
< Y(obs) = the observed amplitude specified by
< _refine_ls_structure_factor_coef
< Y(calc) = the calculated amplitude specified by
< _refine_ls_structure_factor_coef
< w = the least-squares weight
<
< and the sum is taken over the reflections of this class. See
< also _refine_ls_class_R_factor_ definitions.
---
> wR=sum|w|Y(obs)-Y(calc)|^2^|^1/2^/sum|wY(obs)^2^|
> Y(obs)=the observed amplitude specified by
> _refine_ls_structure_factor_coef, Y(calc)=the calculated
> amplitude specified by _refine_ls_structure_factor_coef, w=the
> least-squares weight, and the sum is taken over the specified
> reflections. See also _refine_ls_class_R_factor_ definitions.
8099c7914
< for the reciprocal lattice.
---
> for the reciprocal cell.
8102,8116d7916
< data_refln_d_spacing
< _name '_refln_d_spacing'
< _category refln
< _type numb
< _list yes
< _list_reference '_refln_index_'
< _enumeration_range 0.0:
< _units A
< _units_detail 'angstroms'
< _definition
< ; The d spacing in angstroms for this reflection. It is related
< to the (sin theta)/lambda value by the expression
< _refln_d_spacing = 2/(_refln_sint/lambda)
< ;
<
8139c7939
< measurement) of the structure factors, (in electrons for
---
> measurement) of the structure factors, in electrons (for
8153,8154c7953,7954
< from measurement) of the squared structure factors (in electrons
< squared for X-ray diffraction).
---
> from measurement) of the squared structure factors, in electrons
> squared (for X-ray diffraction).
8161,8162d7960
< _related_item '_refln_observed_status'
< _related_function alternate
8167,8168c7965
< ; (lower-case letter o for 'observed')
< satisfies _refine_ls_d_res_high
---
> ; satisfies _refine_ls_d_res_high
8221d8017
< _enumeration_range 0.0:
8346,8350c8142,8144
< ; The number of reflections symmetry-equivalent under the Laue
< symmetry to the present reflection. In the Laue symmetry, Friedel
< opposites (h k l and -h -k -l) are equivalent. Tables of
< symmetry-equivalent reflections are available in International
< Tables for Crystallography, Volume A (1987), section 10.2.
---
> ; The number of symmetry-equivalent reflections. The equivalent
> reflections have the same structure-factor magnitudes because
> of the space-group symmetry and the Friedel relationship.
8485c8279
< ; Miller indices limits for the reported reflections. These need
---
> ; Miller indices limits for the intensity measurements. These need
8493,8494d8286
< _related_item '_reflns_number_observed'
< _related_function alternate
8518,8522c8310,8313
< (or the deprecated _reflns_observed_criterion). They may include
< Friedel equivalent reflections according to the nature of the
< structure and the procedures used. The special characteristics
< of the reflections included in the _refln_ list should be given
< in the item _reflns_special_details.
---
> (or the deprecated _reflns_observed_criterion). They may
> include Friedel equivalent reflections according to the
> nature of the structure and the procedures used. The item
> _reflns_special_details describes the reflection data.
8536,8538c8327,8328
< used. The special characteristics of the reflections included
< in the _refln_ list should be given in the item
< _reflns_special_details.
---
> used. The item _reflns_special_details describes the reflection
> data.
8559,8562c8349,8350
< ; Description of the properties of the reported reflection list
< that is not given in other data items. In particular it should
< include information about the averaging (or not) of
< symmetry-equivalent reflections including Friedel pairs.
---
> ; A description of reflection data not covered by the other data
> names. It should include details of the Friedel pairs.
8569,8570d8356
< _related_item '+_reflns_observed_criterion'
< _related_function alternate
8676,8681c8462,8464
< equivalent reflections (i.e. those which are symmetry equivalent
< under the Laue symmetry but inequivalent under the crystal
< class) according to the nature of the structure and the
< procedures used. The special characteristics of the reflections
< included in the _refln_ list should be given in the item
< _reflns_special_details.
---
> equivalent reflections according to the nature of the structure
> and the procedures used. The item _reflns_special_details
> describes the reflection data.
8697,8699c8480,8481
< structure and the procedures used. The special characteristics
< of the reflections included in the _refln_ list should be given
< in the item _reflns_special_details
---
> structure and the procedures used. The item
> _reflns_special_details describes the reflection data.
8717,8725c8499,8502
<
< sum | F(obs) - F(calc) |
< R = ------------------------
< sum | F(obs) |
<
< F(obs) = the observed structure-factor amplitudes
< F(calc) = the calculated structure-factor amplitudes
<
< and the sum is taken over the reflections of this class. See also
---
> R=sum|F(obs)-F(calc)|/sum|F(obs)|
> F(obs)=the observed structure-factor amplitudes, F(calc)=the
> calculated structure-factor amplitudes, and the sum is taken over
> the specified reflections. See also
8738,8754c8515,8524
< on the squared amplitudes of the observed and calculated
< structure factors, for the reflections judged significantly
< intense (i.e. satisfying the threshold specified by
< _reflns_threshold_expression) and included in the refinement.
<
< The reflections also satisfy the resolution limits established
< by _reflns_class_d_res_high and _reflns_class_d_res_low.
<
< sum | F(obs)^2^ - F(calc)^2^ |
< R(Fsqd) = -------------------------------
< sum F(obs)^2^
<
< F(obs)^2^ = squares of the observed structure-factor amplitudes
< F(calc)^2^ = squares of the calculated structure-factor
< amplitudes
<
< and the sum is taken over the reflections of this class.
---
> on the squares of the observed and calculated structure factors,
> for the reflections judged significantly intense (i.e. satisfying
> the threshold specified by _reflns_threshold_expression) and
> included in the refinement. The reflections also satisfy the
> resolution limits established by _reflns_class_d_res_high and
> _reflns_class_d_res_low.
> R(F^2^)=sum|F(obs)^2^-F(calc)^2^|/sum|F(obs)^2^|
> F(obs)^2^=squares of the observed structure-factor amplitudes,
> F(calc)^2^=squares of the calculated structure-factor amplitudes,
> and the sum is taken over the specified reflections.
8772,8780c8542,8544
<
< sum | I(obs) - I(calc) |
< R(I) = ------------------------
< sum | I(obs) |
<
< I(obs) = the net observed intensities
< I(calc) = the net calculated intensities
<
< and the sum is taken over the reflections of this class.
---
> R(I)=sum|I(obs)-I(calc)|/sum|I(obs)|
> I(obs)=the net observed intensities, I(calc)=the net calculated
> intensities, and the sum is taken over the specified reflections
8795,8807c8559,8564
<
< ( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
< wR = ( ------------------------------ )
< ( sum w Y(obs)^2^ )
<
< Y(obs) = the observed amplitude specified by
< _refine_ls_structure_factor_coef
< Y(calc) = the calculated amplitude specified by
< _refine_ls_structure_factor_coef
< w = the least-squares weight
<
< and the sum is taken over the reflections of this class. See
< also _reflns_class_R_factor_ definitions.
---
> wR=sum|w|Y(obs)-Y(calc)|^2^|^1/2^/sum|wY(obs)^2^|
> Y(obs)=the observed amplitude specified by
> _reflns_structure_factor_coef, Y(calc)=the calculated
> amplitude specified by _reflns_structure_factor_coef, w=the
> least-squares weight, and the sum is taken over the specified
> reflections. See also _reflns_class_R_factor_ definitions.
8850c8607
< codes need not correspond to those in the _diffrn_scale_ list.
---
> codes may not correspond to those in the _diffrn_scale_ list.
8882c8639
< _reflns_shell_meanI_over_uI_gt
---
> _reflns_shell_meanI_over_sigI_gt
8935,8936d8691
< _related_item '_reflns_shell_meanI_over_uI_all'
< _related_function replace
8948,8949d8702
< _related_item '_reflns_shell_meanI_over_uI_gt'
< _related_function replace
8974,9003d8726
< data_reflns_shell_meanI_over_uI_all
< _name '_reflns_shell_meanI_over_uI_all'
< _category reflns_shell
< _type numb
< _related_item '_reflns_shell_meanI_over_sigI_all'
< _related_function alternate
< _list yes
< _definition
< ; The ratio of the mean of the intensities of all reflections
< in this shell to the mean of the standard uncertainties of the
< intensities of all reflections in the resolution shell.
< ;
<
< data_reflns_shell_meanI_over_uI_gt
< _name '_reflns_shell_meanI_over_uI_gt'
< _category reflns_shell
< _type numb
< loop_ _related_item
< _related_function '_reflns_shell_meanI_over_sigI_gt' alternate
< '_reflns_shell_meanI_over_sigI_obs' alternate
< _list yes
< _definition
< ; The ratio of the mean of the intensities of the significantly
< intense reflections (see _reflns_threshold_expression) in
< this shell to the mean of the standard uncertainties of the
< intensities of the significantly intense reflections in the
< resolution shell.
< ;
<
<
9009d8731
< _enumeration_range 0.0:
9019,9020d8740
< _related_item '_reflns_shell_number_measured_obs'
< _related_function alternate
9022d8741
< _enumeration_range 0.0:
9036d8754
< _enumeration_range 0.0:
9070,9071d8787
< _related_item '_reflns_shell_number_unique_obs'
< _related_function alternate
9101c8817
< _enumeration_range 0.0:100.0
---
> _enumeration_range 0.0:
9112,9113d8827
< _related_item '_reflns_shell_percent_possible_obs'
< _related_function alternate
9115c8829
< _enumeration_range 0.0:100.0
---
> _enumeration_range 0.0:
9130c8844
< _enumeration_range 0.0:100.0
---
> _enumeration_range 0.0:
9163,9164d8876
< _related_item '_reflns_shell_Rmerge_F_obs'
< _related_function alternate
9232,9233d8943
< _related_item '_reflns_shell_Rmerge_I_obs'
< _related_function alternate
==============================================================================
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