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Core CIF - revision to accommodate Acta C Notes for Authors
- To: COMCIFS@iucr
- Subject: Core CIF - revision to accommodate Acta C Notes for Authors
- From: Brian McMahon <[email protected]>
- Date: Mon Nov 17 11:55:40 1997
As far back as the beginning of the year, COMCIFS gave implicit approval
for the introduction of new data names required by Acta Crystallographica
Section C (see circular 54). These were mostly changes of nomenclature to
deprecate the use of the terms "thermal displacement", "estimated standard
deviation" and "observed". These changes have been worked up into formal
definitions which are listed in an appendix to this mailing. There is one
additional data name that falls outside of this group, and that is
"_reflns_number_Friedel". I would ask you to check through these
definitions, and let me know of any errors, ambiguities or lacunae. I shall
post the complete dictionary on the web as version 2.1beta1 on 28 November,
to permit general public scrutiny, and request formal approval at the
beginning of 1998. This is a convenient opportunity to submit additional
data items that you feel are lacking from the Core.
##############################################################################
APPENDIX Changes to the core CIF Dictionary
The core dictionary is a large enough document that it is inconvenient to
post, and difficult enough to extract unambiguously the changes between
versions. I therefore include here some indications of the changes that
have been made, but encourage you to download and look at the full version
to resolve any ambiguities that you find. the full version is at
ftp://ftp.iucr.org/cifdics/cif_core_2.1beta.dic
The following data blocks have been modified. ("<" flags data blocks that
have been deleted, ">" ones that have been added. Deletions from the older
dictionary file indicate that a composite definition has been broken up into
multiple definitions in the newer dictionary - for example to indicate that
an "..._obs" data name should be replaced by a "..._gt" one.)
> data_atom_site_adp_type
> data_diffrn_measured_fraction_theta_full
> data_diffrn_measured_fraction_theta_max
> data_diffrn_detector_area_resol_mean
< data_diffrn_reflns_theta_
> data_diffrn_reflns_theta_full
> data_diffrn_reflns_theta_max
> data_diffrn_reflns_theta_min
< data_refine_ls_goodness_of_fit_
> data_refine_ls_goodness_of_fit_all
> data_refine_ls_goodness_of_fit_gt
> data_refine_ls_goodness_of_fit_obs
> data_refine_ls_goodness_of_fit_ref
< data_refine_ls_R_factor_
> data_refine_ls_R_factor_all
> data_refine_ls_R_factor_gt
> data_refine_ls_R_factor_obs
< data_refine_ls_restrained_S_
< data_refine_ls_shift/esd_
> data_refine_ls_restrained_S_all
> data_refine_ls_restrained_S_gt
> data_refine_ls_restrained_S_obs
> data_refine_ls_shift/esd_max
> data_refine_ls_shift/esd_mean
> data_refine_ls_shift/su_max
> data_refine_ls_shift/su_mean
< data_refine_ls_wR_factor_
> data_refine_ls_wR_factor_all
> data_refine_ls_wR_factor_gt
> data_refine_ls_wR_factor_obs
> data_refine_ls_wR_factor_ref
> data_refln_include_status
< data_reflns_number_
> data_reflns_number_Friedel
> data_reflns_number_gt
> data_reflns_number_observed
> data_reflns_number_total
> data_reflns_threshold_expression
> data_reflns_shell_meanI_over_sigI_gt
> data_reflns_shell_number_measured_gt
> data_reflns_shell_number_unique_gt
> data_reflns_shell_percent_possible_gt
> data_reflns_shell_Rmerge_F_gt
> data_reflns_shell_Rmerge_I_gt
The following definitions are new (the unusual layout here is a feature of
the software I have used to extract these items from the full dictionary
file):
data_atom_site_adp_type
_name '_atom_site_adp_type'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
loop_
_enumeration
_enumeration_detail
Uani 'anisotropic Uij'
Uiso 'isotropic U'
Uovl 'overall U'
Umpe 'multipole expansion U'
Bani 'anisotropic Bij'
Biso 'isotropic B'
Bovl 'overall B'
_definition
; A standard code used to describe the type of atomic displacement
parameters used for the site.
;
data_diffrn_measured_fraction_theta_full
_name '_diffrn_measured_fraction_theta_full'
_category diffrn
_list yes
_type numb
_enumeration_range 0:1.0
_definition
; Fraction of unique (symmetry-independent) reflections measured
out to _diffrn_reflns_theta_full.
;
data_diffrn_measured_fraction_theta_max
_name '_diffrn_measured_fraction_theta_max'
_category diffrn
_list yes
_type numb
_enumeration_range 0:1.0
_definition
; Fraction of unique (symmetry-independent) reflections measured
out to _diffrn_reflns_theta_max.
;
data_diffrn_detector_area_resol_mean
_name '_diffrn_detector_area_resol_mean'
_category diffrn_detector
_type numb
_enumeration_range 0.0:
_units mm^-1^
_units_detail 'pixels per millimetre'
_definition
; The resolution of an area detector, in pixels/mm.
;
data_diffrn_reflns_theta_full
_name '_diffrn_reflns_theta_full'
_category diffrn_reflns
_type numb
_enumeration_range 0.0:90.0
_units deg
_units_detail 'degrees'
_definition
; 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
_diffrn_measured_fraction_theta_full.
;
data_refine_ls_goodness_of_fit_gt
_name '_refine_ls_goodness_of_fit_gt'
_category refine
_type numb
_type_conditions esd
_enumeration_range 0.0:
_definition
; The least-squares goodness-of-fit parameter S for
significantly intense reflections, (see
_reflns_threshold_expression), after the final cycle of
refinement. Ideally, account should be taken of parameters
restrained in the least squares. See also
_refine_ls_restrained_S_ definitions.
{ sum | w | Y(obs) - Y(calc) |^2^ | }^1/2^
S = { ----------------------------------- }
{ Nref - Nparam }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(sigma squared)]
sigma = standard uncertainty
Nref = the number of reflections used in the refinement
Nparam = the number of refined parameters
and the sum is taken over the specified reflections
;
data_refine_ls_goodness_of_fit_ref
_name '_refine_ls_goodness_of_fit_ref'
_category refine
_type numb
_type_conditions esd
_enumeration_range 0.0:
_definition
; The least-squares goodness-of-fit parameter S for all
reflections included in the refinement, after the final cycle
of refinement. Ideally, account should be taken of parameters
restrained in the least squares. See also
_refine_ls_restrained_S_ definitions.
{ sum | w | Y(obs) - Y(calc) |^2^ | }^1/2^
S = { ----------------------------------- }
{ Nref - Nparam }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(sigma squared)]
sigma = standard uncertainty
Nref = the number of reflections used in the refinement
Nparam = the number of refined parameters
and the sum is taken over the specified reflections
;
data_refine_ls_R_factor_gt
_name '_refine_ls_R_factor_gt'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; Residual factor for the reflections (with number given by
_reflns_number_gt) 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_d_res_high and
_refine_ls_d_res_low. This is the conventional R
factor. See also _refine_ls_wR_factor_ definitions.
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 specified reflections
;
data_refine_ls_restrained_S_gt
_name '_refine_ls_restrained_S_gt'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; The least-squares goodness-of-fit parameter S' for
significantly intense reflections (satisfying
_reflns_threshold_expression) after the final cycle
of least squares. This parameter explicitly includes
the restraints applied in the least-squares process.
See also _refine_ls_goodness_of_fit_ definitions.
{sum | w | Y(obs) - Y(calc) |^2^ | )^1/2^
( + sum~r~ | w~r~ | P(calc) - P(targ) |^2^ | }
S' = { -------------------------------------------------- }
{ N~ref~ + N~restr~ - N~param~ }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the observed coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/square of standard uncertainty (e.s.d.)]
P(calc) = the calculated restraint values
P(targ) = the target restraint values
w~r~ = the restraint weight
N~ref~ = the number of reflections used in the refinement
(see _refine_ls_number_reflns)
N~restr~ = the number of restraints
(see _refine_ls_number_restraints)
N~param~ = the number of refined parameters
(see _refine_ls_number_parameters)
sum is taken over the specified reflections
sum~r~ is taken over the restraints
;
data_refine_ls_shift/su_max
_name '_refine_ls_shift/su_max'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; The largest ratio of the final least-squares parameter
shift divided by the final standard uncertainty.
;
data_refine_ls_shift/su_mean
_name '_refine_ls_shift/su_mean'
_category refine
_type numb
_related_item '_refine_ls_shift/su_mean'
_related_purpose replace
_enumeration_range 0.0:
_definition
; The average ratio of the final least-squares parameter
shift divided by the final standard uncertainty.
;
data_refine_ls_wR_factor_gt
_name '_refine_ls_wR_factor_gt'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; Weighted residual factors for significantly intense reflections
(satisfying _reflns_threshold_expression) included in the
refinement. The reflections also satisfy the resolution
limits established by _refine_ls_d_res_high and
_refine_ls_d_res_low. See also the _refine_ls_R_factor_
definitions.
( sum | w | Y(obs) - Y(calc) |^2^ | )^1/2^
wR = ( --------------------------------- )
( sum | w Y(calc)^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
;
data_refine_ls_wR_factor_ref
_name '_refine_ls_wR_factor_ref'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; Weighted residual factors for all reflections included in the
refinement. The reflections also satisfy the resolution
limits established by _refine_ls_d_res_high and
_refine_ls_d_res_low. See also the _refine_ls_R_factor_
definitions.
( sum | w | Y(obs) - Y(calc) |^2^ | )^1/2^
wR = ( --------------------------------- )
( sum | w Y(calc)^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
;
data_refln_include_status
_name '_refln_include_status'
_category refln
_type char
_list yes
_list_reference '_refln_index_'
loop_
_enumeration
_enumeration_detail
o
; satisfies _refine_ls_d_res_high
satisfies _refine_ls_d_res_low
exceeds _reflns_threshold_expression
;
<
; satisfies _refine_ls_d_res_high
satisfies _refine_ls_d_res_low
does not exceed
_reflns_threshold_expression
;
- 'systematically absent reflection'
x 'unreliable measurement -- not used'
h 'does not satisfy _refine_ls_d_res_high'
l 'does not satisfy _refine_ls_d_res_low'
_enumeration_default o
_definition
; Classification of a reflection so as to indicate its status with
respect to inclusion in refinement and calculation of R factors.
;
data_reflns_number_Friedel
_name '_reflns_number_Friedel'
_category reflns
_type numb
_enumeration_range 0:
_definition
; The number of Friedel equivalent reflections in the _refln_
list. Friedel equivalent reflections may be treated as
independent reflections in the least-squares refinement
because, although related by symmetry, they may differ in
intensity owing to inelastic scattering.
;
data_reflns_number_gt
_name '_reflns_number_gt'
_category reflns
_type numb
_enumeration_range 0:
_definition
; The number of reflections in the _refln_ list (not the
_diffrn_refln_ list) that are significantly intense,
satisfying the criterion specified by
_reflns_threshold_expression. 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.
;
data_reflns_threshold_expression
_name '_reflns_threshold_expression'
_category reflns
_type char
_example 'I>2\s(I)'
_definition
; The threshold, based on multiples of \s(I), \s(F^2^) or \s(F),
that serves to identify significantly intense reflections,
the number of which is given by _reflns_number_gt. These
reflections are used in the calculation of
_refine_ls_R_factor_gt.
;
data_reflns_shell_meanI_over_sigI_gt
_name '_reflns_shell_meanI_over_sigI_gt'
_category reflns_shell
_type numb
_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.
;
data_reflns_shell_number_measured_gt
_name '_reflns_shell_number_measured_gt'
_category reflns_shell
_type numb
_list yes
_definition
; The number of significantly intense reflections
(see _reflns_threshold_expression) measured for this
resolution shell.
;
data_reflns_shell_number_unique_gt
_name '_reflns_shell_number_unique_gt'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0:
_definition
; The total number of significantly intense reflections
(see _reflns_threshold_expression) which are
symmetrically unique after merging for this resolution shell.
;
data_reflns_shell_percent_possible_gt
_name '_reflns_shell_percent_possible_gt'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0.0:
_definition
; The percentage of geometrically possible reflections
represented by significantly intense reflections
(see _reflns_threshold_expression) measured for this
resolution shell.
;
data_reflns_shell_Rmerge_F_gt
_name '_reflns_shell_Rmerge_F_gt'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0.0:
_definition
; The value of Rmerge(F) for significantly intense reflections
(see _reflns_threshold_expression) in a given shell.
sum~i~ ( sum~j~ | F~j~ - <F> | )
Rmerge(F) = --------------------------------
sum~i~ ( sum~j~ <F> )
F~j~ = the amplitude of the jth observation of reflection i
<F> = the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
data_reflns_shell_Rmerge_I_gt
_name '_reflns_shell_Rmerge_I_gt'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0.0:
_definition
; The value of Rmerge(I) for significantly intense reflections
(see _reflns_threshold_expression) in a given shell.
sum~i~ ( sum~j~ | I~j~ - <I> | )
Rmerge(I) = --------------------------------
sum~i~ ( sum~j~ <I> )
I~j~ = the intensity of the jth observation of reflection i
<I> = the mean of the intensities of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
##############################################################################
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