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Re: Transfer from msCIF: refine_ls_class category
- To: Multiple recipients of list <coredmg@iucr.org>
- Subject: Re: Transfer from msCIF: refine_ls_class category
- From: Brian McMahon <bm@iucr.org>
- Date: Thu, 10 Sep 1998 16:16:36 +0100 (BST)
Here (at the end of the message) is my attempt at moving the various
categories that relate to reflection classes from the msCIF draft to the
core. I have reworded some definitions to suggest that there is freedom
to assign classes to suit various requirements, but as yet the examples
are all taken from the modulated structures examples.
I am a bit confused about the proper assignment of parent/child
relationships between the new categories. The following diagram indicates
what is done (based largely on Gotzon's original proposals). Two new
pointers have been introduced to existing categories (_refln_class_code and
_diffrn_refln_class_code). The relationships illustrated are "has as parent"
(i.e. _diffrn_reflns_class_code is the parent of the four other data names
indicated, _reflns_class_code is the parent of _refln_class_code). A parent
may have several children; a child can have only one parent.
It seems to me that what this relationship is showing is that the senior
category here is DIFFRN_REFLNS_CLASS, a description of the different groups
of reflections assigned on the raw diffractogram. Individual reflections in
each group are identified through the _diffrn_refln_class_code. REFLNS_CLASS
is a subsidiary category, giving details of the matching groups of
reflections in the structure-factor list. I have thought it useful (or at
least consistent) to allow identification of the individual reflections
through the _refln_class_code.
Now REFLNS_SHELL_CLASS and REFINE_LS_CLASS also appear as subsidiary
categories of the DIFFRN_REFLNS_CLASS one. Does this seem appropriate?
Or should these be linked to the REFLNS_CLASS category instead?
####################################
## EXISTING CATEGORY DIFFRN_REFLN ##
####################################
_diffrn_refln_class_code ----------------------
##################################### |
## EXISTING CATEGORY DIFFRN_REFLNS ## |
##################################### |
_diffrn_reflns_number_of_classes |
######################### |
## DIFFRN_REFLNS_CLASS ## |
######################### |
_diffrn_reflns_class_[] |
_diffrn_reflns_class_av_R_eq |
_diffrn_reflns_class_av_sgI/I |
* _diffrn_reflns_class_code <=======================----
_diffrn_reflns_class_number_of_reflns | | |
_diffrn_reflns_class_d_res_high | | |
_diffrn_reflns_class_d_res_low | | |
_diffrn_reflns_class_description | | |
##################### | | |
## REFINE_LS_CLASS ## | | |
##################### | | |
_refine_ls_class_[] | | |
* _refine_ls_class_code ---------------->----------- | |
_refine_ls_class_d_res_high | |
_refine_ls_class_d_res_low | |
_refine_ls_class_R_factor_all | |
_refine_ls_class_R_factor_gt | |
_refine_ls_class_R_Fsqd_factor | |
_refine_ls_class_R_I_factor | |
_refine_ls_class_wR_factor_all | |
############################# | |
## EXISTING CATEGORY REFLN ## | |
############################# | |
_refln_class_code --->-- | |
################## | | |
## REFLNS_CLASS ## | | |
################## | | |
_reflns_class_[] | | |
<---- | |
* _reflns_class_code ------------------->-------------- |
_reflns_class_number_of_reflns_total |
_reflns_class_number_of_reflns_gt |
######################## |
## REFLNS_SHELL_CLASS ## |
######################## |
_reflns_shell_class_[] |
* _reflns_shell_class_code ------------->---------------
_reflns_shell_class_d_res_high
_reflns_shell_class_d_res_low
_reflns_shell_class_meanI_over_sigI_all
_reflns_shell_class_meanI_over_sigI_gt
_reflns_shell_class_number_measured_all
_reflns_shell_class_number_measured_gt
_reflns_shell_class_number_possible
_reflns_shell_class_number_unique_all
_reflns_shell_class_number_unique_gt
_reflns_shell_class_percent_possible_all
_reflns_shell_class_percent_possible_gt
_reflns_shell_class_Rmerge_F_all
_reflns_shell_class_Rmerge_F_gt
_reflns_shell_class_Rmerge_I_all
_reflns_shell_class_Rmerge_I_gt
I note also that the DIFFRN_REFLNS category has the new dataname
_diffrn_reflns_number_of_classes. There is, however, no matching
_reflns_number_of_classes in the REFLNS category. Should there be?
Regards
Brian
==============================================================================
####################################
## EXISTING CATEGORY DIFFRN_REFLN ##
####################################
data_diffrn_refln_class_code
_name '_diffrn_refln_class_code'
_category diffrn_refln
_type char
_list yes
_list_reference '_diffrn_refln_index_'
_list_link_parent '_diffrn_reflns_class_code'
_definition
; The code identifying the class to which this reflection has been
assigned. This code must match a value of
_diffrn_reflns_class_code. Reflections may be grouped into
classes for a variety of purposes. For example, for modulated
structures each reflection class may be
defined by the number m=sum|mi|, where the mi are the integer
coefficients that, in addition to h,k,l, index the corresponding
diffraction vector in the basis defined for the reciprocal cell.
;
####################################
## EXISTING CATEGORY DIFFRN_REFLN ##
####################################
data_diffrn_reflns_number_of_classes
_name '_diffrn_reflns_number_of_classes'
_category diffrn_reflns
_type numb
_definition
; Number of different intensity classes measured. Reflections
may be grouped into classes for a variety of purposes. For
example, for modulated structures each reflection class may
be defined by the number m=sum|mi|, where the mi are the
integer coefficients that, in addition to h,k,l, index the
corresponding diffraction vector in the basis defined for the
reciprocal cell.
;
#########################
## DIFFRN_REFLNS_CLASS ##
#########################
data_diffrn_reflns_class_[]
_name '_diffrn_reflns_class_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_diffrn_reflns_class_number_of_reflns
_diffrn_reflns_class_d_res_high
_diffrn_reflns_class_d_res_low
_diffrn_reflns_class_av_R_eq
_diffrn_reflns_class_code
_diffrn_reflns_class_description
1580 0.551 6.136 0.015 'Main' 'm=0; main reflections'
1045 0.551 6.136 0.010 'Sat1' 'm=1; first-order satellites'
;
;
Example 1 - example corresponding to the one-dimensional incommensurately
modulated structure of K~2~SeO~4~. Each reflection class is
defined by the number m=sum|mi|, where the mi are the integer
coefficients that, in addition to h,k,l, index the
corresponding diffraction vector in the basis defined for the
reciprocal cell.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_REFLNS_CLASS category record details
about the classes of reflections measured in the diffraction
experiment.
;
data_diffrn_reflns_class_av_R_eq
_name '_diffrn_reflns_class_av_R_eq'
_category diffrn_reflns_class
_type numb
_list yes
_list_reference '_diffrn_reflns_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, 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 individual
intensities.
;
data_diffrn_reflns_class_av_sgI/I
_name '_diffrn_reflns_class_av_sgI/I'
_category diffrn_reflns_class
_type numb
_list yes
_list_reference '_diffrn_reflns_class_code'
_enumeration_range 0.0:
_definition
; Measure [sum|sigma(I)|/sum|net(I)|] for all measured intensities
in a reflection class.
;
data_diffrn_reflns_class_code
_name '_diffrn_reflns_class_code'
_category diffrn_reflns_class
_type char
_list yes
_list_mandatory yes
loop_ _list_link_child '_diffrn_refln_class_code'
'_refine_ls_class_code'
'_reflns_class_code'
'_reflns_shell_class_code'
loop_ _example '1'
'm1'
's2'
_definition
; The code identifying a certain reflection class.
;
data_diffrn_reflns_class_number_of_reflns
_name '_diffrn_reflns_class_number_of_reflns'
_category diffrn_reflns_class
_type numb
_list yes
_list_reference '_diffrn_reflns_class_code'
_enumeration_range 0:
_definition
; The total number of measured intensities for each reflection
class, excluding the systematic extinctions arising from
centering translations.
;
data_diffrn_reflns_class_d_res_
loop_ _name '_diffrn_reflns_class_d_res_high'
'_diffrn_reflns_class_d_res_low'
_category diffrn_reflns_class
_type numb
_list yes
_list_reference '_diffrn_reflns_class_code'
_enumeration_range 0.0:
_units A
_units_detail 'Angstroms'
_definition
; The highest and lowest resolution in angstroms for the
interplanar spacing in the reflections of each measured
reflection class. They are the smallest and the highest d values
for each reflection class.
;
data_diffrn_reflns_class_description
_name '_diffrn_reflns_class_description'
_category diffrn_reflns_class
_type char
_list yes
_list_reference '_diffrn_reflns_class_code'
loop_ _example 'm=1 first order satellites'
'H0L0 common projection reflections'
_definition
; Description of each reflection class. Number of definitions must
match the number given in _diffrn_reflns_number_of_classes.
;
#####################
## REFINE_LS_CLASS ##
#####################
data_refine_ls_class_[]
_name '_refine_ls_class_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_refine_ls_class_R_factor_gt
_refine_ls_class_code
0.057 'Main'
0.074 'Com'
0.064 'NbRefls'
0.046 'LaRefls'
0.112 'Sat1'
0.177 'Sat2'
;
;
Example 1 - example for a modulated structure extracted from van Smaalen
[(1991). J. Phys.:Condens. Matter, 3, 1247-1263.]
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the REFINE_LS_CLASS category record details
(for each reflection class separately) about the reflections used
for the structure refinement.
;
data_refine_ls_class_code
_name '_refine_ls_class_code'
_category refine_ls_class
_type char
_list yes
_list_link_parent '_diffrn_reflns_class_code'
loop_ _example '1'
'm1'
's2'
_definition
; The code identifying a certain reflection class. This code must
match a _diffrn_reflns_class_code.
;
data_refine_ls_class_d_res_high
_name '_refine_ls_class_d_res_high'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_units A
_units_detail 'Angstroms'
_definition
; For each reflection class, the highest resolution in angstroms
for the spacing in the reflections used in refinement. This is
the lowest d value in a reflection class.
;
data_refine_ls_class_d_res_low
_name '_refine_ls_class_d_res_low'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_units A
_units_detail 'Angstroms'
_definition
; For each reflection class, the lowest resolution in angstroms
for the spacing in the reflections used in refinement. This is
the highest d value in a reflection class.
;
data_refine_ls_class_R_factor_
loop_ _name '_refine_ls_class_R_factor_all'
'_refine_ls_class_R_factor_gt'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the residual factors for all
reflections, and for significantly intense reflections (see
_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.
This is the conventional R factor.
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
_refine_ls_class_wR_factor_all definitions.
;
data_refine_ls_class_R_Fsqd_factor
_name '_refine_ls_class_R_Fsqd_factor'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the residual factor R(F^2^) calculated
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.
;
data_refine_ls_class_R_I_factor
_name '_refine_ls_class_R_I_factor'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the residual factor R(I) for the
reflections judged significantly intense (i.e. satisfying the
threshold specified by _reflns_threshold_expression) and
included in the refinement.
This is most often calculated in Rietveld refinements
of powder data, where it is referred to as R~B~ or R~Bragg~
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
;
data_refine_ls_class_wR_factor_all
_name '_refine_ls_class_wR_factor_all'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the weighted residual factors for all
reflections 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.
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.
;
#############################
## EXISTING CATEGORY REFLN ##
#############################
data_refln_class_code
_name '_refln_class_code'
_category refln
_type char
_list yes
_list_reference '_refln_index_'
_list_link_parent '_reflns_class_code'
_definition
; The code identifying the class to which this reflection has been
assigned. This code must match a value of _reflns_class_code.
Reflections may be grouped into classes for a variety of purposes.
For example, for modulated structures each reflection class may be
defined by the number m=sum|mi|, where the mi are the integer
coefficients that, in addition to h,k,l, index the corresponding
diffraction vector in the basis defined for the reciprocal cell.
;
##################
## REFLNS_CLASS ##
##################
data_reflns_class_[]
_name '_reflns_class_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_reflns_class_number_of_reflns_gt
_reflns_class_code
584 'Main'
226 'Sat1'
50 'Sat2'
;
;
Example 1 - example corresponding to the one-dimensional incommensurately
modulated structure of K~2~SeO~4~.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the REFLNS_CLASS category record details, for
each reflection class, about the reflections used to determine
the structural parameters.
;
data_reflns_class_code
_name '_reflns_class_code'
_category reflns_class
_type char
_list yes
_list_link_child '_refln_class_code'
_list_link_parent '_diffrn_reflns_class_code'
loop_ _example '1'
'm1'
's2'
_definition
; The code identifying a certain reflection class. This code must
match a _diffrn_reflns_class_code.
;
data_reflns_class_number_of_reflns_
loop_ _name '_reflns_class_number_of_reflns_total'
'_reflns_class_number_of_reflns_gt'
_category reflns_class
_type numb
_list yes
_list_reference '_reflns_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the total number of reflections, and
the number of significantly intense reflections (see
_reflns_threshold_expression) in the _refln_ list (not the
_diffrn_refln_ list). 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.
;
########################
## REFLNS_SHELL_CLASS ##
########################
data_reflns_shell_class_[]
_name '_reflns_shell_class_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
No example
;
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the REFLNS_SHELL_CLASS category record details, for
each reflection class, about the reflections used to determine
the structural parameters, as broken down by shells of
resolution.
;
data_reflns_shell_class_code
_name '_reflns_shell_class_code'
_category reflns_shell_class
_type char
_list yes
_list_link_parent '_diffrn_reflns_class_code'
loop_ _example '1'
'm1'
's2'
_definition
; The code identifying a certain reflection class. This code must
match a _diffrn_reflns_class_code.
;
data_reflns_shell_class_d_res_high
_name '_reflns_shell_class_d_res_high'
_category reflns_shell_class
_type numb
_list yes
_list_reference '_reflns_shell_class_code'
_enumeration_range 0.0:
_units A
_units_detail 'Angstroms'
_definition
; For each reflection class the highest resolution in angstroms for
the interplanar spacing in the reflections in this shell. This is
the smallest d value.
;
data_reflns_shell_class_d_res_low
_name '_reflns_shell_class_d_res_low'
_category reflns_shell_class
_type numb
_list yes
_list_reference '_reflns_shell_class_code'
_enumeration_range 0.0:
_units A
_units_detail 'Angstroms'
_definition
; For each reflection class the lowest resolution in angstroms for
the interplanar spacing in the reflections in this shell. This is
the largest d value.
;
data_reflns_shell_class_meanI_over_sigI_all
_name '_reflns_shell_class_meanI_over_sigI_all'
_category reflns_shell_class
_type numb
_list yes
_list_reference '_reflns_shell_class_code'
_definition
; For each reflection class 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_class_meanI_over_sigI_gt
_name '_reflns_shell_class_meanI_over_sigI_gt'
_category reflns_shell_class
_type numb
_list yes
_list_reference '_reflns_shell_class_code'
_definition
; For each reflection class the ratio of the mean of the
intensities of the reflections judged significantly intense (see
_reflns_threshold_expression) in this shell to the mean of the
standard uncertainties of the significantly intense reflections
in the resolution shell.
;
data_reflns_shell_class_number_measured_all
_name '_reflns_shell_class_number_measured_all'
_category reflns_shell_class
_type numb
_list yes
_list_reference '_reflns_shell_class_code'
_enumeration_range 0:
_definition
; For each reflection class the total number of reflections
measured for this resolution shell.
;
data_reflns_shell_class_number_measured_gt
_name '_reflns_shell_class_number_measured_gt'
_category reflns_shell_class
_type numb
_list yes
_list_reference '_reflns_shell_class_code'
_enumeration_range 0:
_definition
; For each reflection class the number of reflections judged
significantly intense (see _reflns_threshold_expression) measured
for this resolution shell.
;
data_reflns_shell_class_number_possible
_name '_reflns_shell_class_number_possible'
_category reflns_shell_class
_type numb
_list yes
_list_reference '_reflns_shell_class_code'
_enumeration_range 0:
_definition
; For each reflection class the number of unique reflections it is
possible to measure in this reflection shell.
;
data_reflns_shell_class_number_unique_all
_name '_reflns_shell_class_number_unique_all'
_category reflns_shell_class
_type numb
_list yes
_list_reference '_reflns_shell_class_code'
_enumeration_range 0:
_definition
; For each reflection class the total number of measured
reflections remaining after merging symmetry equivalent
reflections for this resolution shell.
;
data_reflns_shell_class_number_unique_gt
_name '_reflns_shell_class_number_unique_gt'
_category reflns_shell_class
_type numb
_list yes
_list_reference '_reflns_shell_class_code'
_enumeration_range 0:
_definition
; For each reflection class the total number of reflections
judged significantly intense (see _reflns_threshold_expression)
remaining after merging symmetry equivalent reflections for this
resolution shell.
;
data_reflns_shell_class_percent_possible_all
_name '_reflns_shell_class_percent_possible_all'
_category reflns_shell_class
_type numb
_list yes
_list_reference '_reflns_shell_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class the percentage of geometrically
possible reflections represented by all reflections measured for
this resolution shell.
;
data_reflns_shell_class_percent_possible_gt
_name '_reflns_shell_class_percent_possible_gt'
_category reflns_shell_class
_type numb
_list yes
_list_reference '_reflns_shell_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class the percentage of geometrically
possible reflections represented by significantly intense
reflections (see _reflns_threshold_expression) measured for this
resolution shell.
;
data_reflns_shell_class_Rmerge_F_all
_name '_reflns_shell_class_Rmerge_F_all'
_category reflns_shell_class
_type numb
_list yes
_list_reference '_reflns_shell_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class the value of Rmerge(F) for all
reflections 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_class_Rmerge_F_gt
_name '_reflns_shell_class_Rmerge_F_gt'
_category reflns_shell_class
_type numb
_list yes
_list_reference '_reflns_shell_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class the value of Rmerge(F) for reflections
judged significantly intense (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_class_Rmerge_I_all
_name '_reflns_shell_class_Rmerge_I_all'
_category reflns_shell_class
_type numb
_list yes
_list_reference '_reflns_shell_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class the value of Rmerge(I) for all
reflections 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.
;
data_reflns_shell_class_Rmerge_I_gt
_name '_reflns_shell_class_Rmerge_I_gt'
_category reflns_shell_class
_type numb
_list yes
_list_reference '_reflns_shell_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class 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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