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CIF core revision list 6
- To: Multiple recipients of list <coredmg@iucr.org>
- Subject: CIF core revision list 6
- From: "I. David Brown" <idbrown@mcmail.cis.mcmaster.ca>
- Date: Tue, 13 May 2003 19:18:25 +0100 (BST)
Dear Colleagues,
I enclose the next list (#6) of changes and additions to the core CIF
dictionary for discussion and, if desired, approval. I repeat items in
this list that were not fully approved in list #5, namely items which Syd
Hall and Curt Haltiwanger had questioned. I have now put these into their
final form and request that you check them and, if appropriate, give them
your approval. The other items on list #5, specifically the space group
items, have been transferred to the growing list of approved items. The
only query that was raised was the use of IT in one of the data names to
refer to International Tables. It was suggested that IT now means
information technology and a better name was needed. However, the space
group items have been approved as part of the symmetry CIF dictionary, and
all we can do is decide which of these items should be included in the
core dictionary. We are not allowed to make any changes. The lack of any
other objections means that the space group items in list #5 will now be
included in the revised core dictionary.
In addition to the items held over from list #5, particularly the
extinction items, this list introduces a new category 'atom_type_scat'
designed to add flexibility to the way in which scattering factors are
presented.
Please read through this list carefully and share your comments with the
rest of the Core Dictionary Maintenance Group.
The deadline for comment is
########################
##### 6 JUNE 2003 ####
########################
If you need more time, let me know and I will extend the deadline.
If you have no comments, please indicate your approval (or otherwise) of the
proposed changes. Silence will be taken as approval, though a positive
affirmative vote is much preferred.
Please send your comments to the Core DMG list with the above subject
heading. You can do this most simply do by replying to this email.
David
*****************************************************
Dr.I.David Brown, Professor Emeritus
Brockhouse Institute for Materials Research,
McMaster University, Hamilton, Ontario, Canada
Tel: 1-(905)-525-9140 ext 24710
Fax: 1-(905)-521-2773
idbrown@mcmaster.ca
*****************************************************
LIST #6 OF THE CORE REVISION PROPOSALS CONTAINS THE FOLLOWING ITEMS. FULL
DETAILS ARE GIVEN FOLLOWING THIS INDEX
# Items held over from list #5:
#
# EXPTL_CRYSTAL
# _exptl_crystal_colour_primary
# _exptl_crystal_colour_modifier
# _exptl_crystal_colour_lustre
# _exptl_crystal_density_meas_gt
# _exptl_crystal_density_meas_lt
# _exptl_crystal_density_meas_temp_gt
# _exptl_crystal_density_meas_temp_lt
# _exptl_crystal_recrystallization_method
# REFINE
# _refine_ls_extinction_coef
# _refine_ls_extinction_expression (retire?)
# _refine_ls_extinction_flag
# _refine_ls_extinction_method
#
# Items new to this list
# New category ATOM_TYPE_SCAT
# _atom_type_scat_Cromer_Mann_*
# _atom_type_scat_dispersion_imag
# _atom_type_scat_dispersion_real
# _atom_type_scat_dispersion_source
# _atom_type_scat_factor_id
# _atom_type_scat_factor_type_symbol
# _atom_type_scat_factor_rad_type
# _atom_type_scat_factor_scat_factor_imag
# _atom_type_scat_factor_scat_factor_real
# _atom_type_scat_factor_stol
# _atom_type_scat_length_neutron
# _atom_type_scat_source
#
#############################################
#############################################
#
# Items held over from list #5
#
#################################################
#
# EXPTL_CRYSTAL
#
#################################################
#
# COMMENT: The following three items are based on a scheme developed
# by the ICDD and recommended for use in the powder CIF,
# modified at Syd Hall's suggestion by separating the
# colour into three items each with its own enumeration list.
# Note that the lustres 'dull' and 'clear' are not part of the ICDD standard.
# The enumerated colours are already being checked by PLATON in submissions to
# Acta Cryst.
#
data_exptl_crystal_colour_primary
_name '_exptl_crystal_colour_primary'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
_definition
; The enumeration list of standardized names developed for the
International Center for Diffraction Data.
The colour of a crystal is given by the combination of
_exptl_crystal_colour_modifier with
_exptl_crystal_colour_primary, as in 'dark-green',
'bluish-violet', if necessary combined with
_exptl_crystal_colour_lustre, as in 'metallic-green'.
;
loop_
_enumeration
_enumeration_detail
colourless ?
white ?
black ?
gray ?
brown ?
red ?
pink ?
orange ?
yellow ?
green ?
blue ?
violet ?
data_exptl_crystal_colour_modifier
_name '_exptl_crystal_colour_modifier'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
_definition
; The enumeration list of standardized names developed for the
International Center for Diffraction Data.
The colour of a crystal is given by the combination of
_exptl_crystal_colour_modifier with
_exptl_crystal_colour_primary, as in 'dark-green',
'bluish-violet', if necessary combined with
_exptl_crystal_colour_lustre, as in 'metallic-green'.
;
loop_
_enumeration
_enumeration_detail
light ?
dark ?
whitish ?
blackish ?
grayish ?
brownish ?
reddish ?
pinkish ?
orangish ?
yellowish ?
greenish ?
bluish ?
data_exptl_crystal_colour_lustre
_name '_exptl_crystal_colour_lustre'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
_definition
; The enumeration list of standardized names developed for the
International Center for Diffraction Data.
The colour of a crystal is given by the combination of
_exptl_crystal_colour_modifier with
_exptl_crystal_colour_primary, as in 'dark-green',
'bluish-violet', if necessary combined with
_exptl_crystal_colour_lustre, as in 'metallic-green'.
;
loop_
_enumeration
_enumeration_detail
metallic ?
dull ?
clear ?
# STATUS: Awaiting approval
#
# There were a couple of comments on the next item - see below for details
#
data_exptl_crystal_density_meas_*
loop_ _name
'_exptl_crystal_density_meas_gt'
'_exptl_crystal_density_meas_lt'
_category exptl_crystal
_type numb
_type_conditions esd
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units Mg^-3^
_units_detail 'megagrams per cubic metre'
_definition
; The lower (_*_gt) or upper limit (_*_lt) on the value of the
density measured using standard chemical and physical
methods. The units are megagrams per cubic metre (grams per
cubic centimetre).
;
loop_
_example
_example_detail
'_exptl_crystal_density_meas_lt 1.0'
'specimen floats in water'
'_exptl_crystal_density_meas_gt 2.5 _exptl_crystal_density_meas_lt 5.0'
'Only the range within which the density lies was given in the original paper'
# COMMENT by Syd Hall:
# _exptl_crystal_density_meas_gt _lt
# I don't understand what thresholds "gt" and "lt" have to do with
# density measurements. Do you simply mean the upper and lower limits
# of a range of density measurements e.g. "high" and "low", or is it
# something else?
#
# RESPONSE: Normally a measured density would be a number with an experimental
# uncertainty. If the density were reported as lying between 2.5 and 3.5,
# _*_gt could be set to 2.5 and _*_lt to 3.5. To give the density as 3.0(5)
# implies that 3.0 is more likely than 2.5 or 3.5, which is not what was
# reported. In other cases the density might be reported as being greater
# than 1.0 because the sample sinks in water. In this case _*_gt would be set
# to 1.0. This, and the following item, were suggested by CCDC because the
# present set of items cannot be used to convey the imprecise information that
# sometimes appears in their records. I RECOMMEND that we approve these two
# items.
# COMMENT by Curt Haltiwanger:
# Is this really a measured density or is it an observation related to
# density. Like Syd, the lt and gt made no sense to me until I had read
# David's explanation.
# This suggests that we need more information Presumably the scientist would
# put how less than 1.0 was determined by an entry in
# _exptl_crystal_density_meas_method _exptl_crystal_density_meas_method would
# benefit from additional example - perhaps "sample floats in water" or
# "sample sinks in ethanol"
# The definition should include some examples David's comment make a good
# start on the example
# RESPONSE: A couple of examples have been added.
# STATUS: Awaiting approval
data_exptl_crystal_density_meas_temp_*
loop_
_name '_exptl_crystal_density_meas_temp_gt'
'_exptl_crystal_density_meas_temp_lt'
_category exptl_crystal
_type numb
_type_conditions esd
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units K
_units_detail 'Kelvins'
_definition
; Temperature in kelvins above which (_*_gt) or below which
(_*_lt) _exptl_crystal_density_meas was determined.
;
loop_
_example
_example_detail
'_exptl_crystal_density_meas_temp_lt 300'
; The density was measured as some unspecified temperature below room
temperature.
;
# COMMENT: The above two items suggested by CCDC.
# I have added an example
# STATUS: Awaiting approval
data_exptl_crystal_recrystallization_method
_name '_exptl_crystal_recrystallization_method'
_category exptl_crystal
_type char
_example ?
_definition
; Describes the method used to recrystallize the sample
;
# COMMENT: Suggested by CCDC.
# The name has been changed following Syd Hall's suggestion
# STATUS: Awaiting approval
#########################################
#
# REFINE category
#
#########################################
# The next three items relate to extinction and are an attempt to tighten up
# our definitions.
#
# COMMENT from Syd Hall:
# _refine_ls_extinction_ etc.
#
# As above, enumeration is the key and what
# would be much better is to carefully enumerate _refine_ls_extinction_method
# to identify the widely used approaches. This simplifies both searching
# and validation... and future expansion for new methods.
#
# By the way, the reason for _refine_ls_extinction_expression is because
# there were a number of different "Zach" expressions in use by various
# packages at one stage... and it may well be still the case!
#
# RESPONSE: The present dictionary contains the three items
# _refine_ls_extinction_coef
# _refine_ls_extinction_expression
# _refine_ls_extinction_method
#
# In this proposal I have adapted Syd's suggestion by introducing
#
# _refine_ls_extinction_flag
#
# and I have modified _*_coef and _*_method. _*_expression is now redundant
# and can be retired. The enumeration list of standard corrections appears
# under _*_flag. Each of these flags is accompanied by a description giving
# the expression used to make the correction and define which variable is
# given in _*_coef. A program, having identified the method from _*_flag
# would know which expression has been used and how to use _*_coef. This
# approach would permit easy extension to the methods that will be available
# in DDL3.
#
# In the case where a non-standard method has been used, full details would be
# given in the current item _*_method which has been modified by omitting the
# enumeration default (which never made sense anyway) and the examples (which
# no longer apply). The description can been changed to recognize that this
# item will not be used when _*_flag is used (though it would not be
# syntactically (or semantically) incorrect if it were), hence the name does
# not need to change. Some of the details given in the description of _*_coef
# are now transferred to _*_flag but the meaning has not changed.
#
# Can someone please supply the appropriate expressions for the extinction
# corrections identified in the enumeration list of _*_flag?
#
data_refine_ls_extinction_coef
_name '_refine_ls_extinction_coef'
_category refine
_type numb
_type_conditions esd
_example 3472(52)
_example_detail 'Zachariasen coefficient r* = 0.347(5) E04'
_definition
; The extinction coefficient used to calculate the correction
factor applied to the structure-factors. The nature of the
extinction coefficient is given in the definitions in
_refine_ls_extinction_flag or refine_ls_extinction_method.
Note that the magnitude of these values is usually of the
order of 10000.
;
data_refine_ls_extinction_expression
_name '_refine_ls_extinction_expression'
#
# this item is no longer needed and can be retired.
#
data_refine_ls_extinction_flag
_name '_refine_ls_extinction_flag'
_category refine
_type char
_definition
; A flag identifying the expression used for the extinction
correction applied using the parameter given in
_refine_ls_extinction_coef.
;
loop_
_enumeration
_enumeration_details
Zach
; Zachariasen formula:
(details of formula needed here - if more than one formula is in use, each
should be given a separate enumeration name)
Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.
Larson, A. C. (1967). Acta Cryst. 23, 664-665.
;
BC_1_L
; Becker-Coppens type 1 with Lorentzian mosaic spread
(details of formula needed here)
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst.
A30, 129-153.
;
BC_1_G
; Becker-Coppens type 1 with Gaussian mosaic spread
(details of formula needed here)
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst.
A30, 129-153.
;
BC_2_L
; Becker-Coppens type 2 with Lorentzian mosaic spread
(details of formula needed here)
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst.
A30, 129-153.
;
BC_2_G
; Becker-Coppens type 2 with Gaussian mosaic spread
(details of formula needed here)
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst.
A30, 129-153.
;
data_refine_ls_extinction_method
_name '_refine_ls_extinction_method'
_category refine
_type char
loop_ _example ?
_definition
; A description of the extinction correction method applied when
the method used cannot be identified by one of the flags in
_refine_ls_extinction_flag. The description should contain
all the details needed to repeat the correction.
;
# STATUS: Awaiting approval
####################################
#
# New category ATOM_TYPE_SCAT
#
####################################
#
# COMMENT: The atom_type_scat category is
# being added to allow the real and imaginary components of the scattering
# factors to be given as a function of sin(theta)/lambda in machine readable
# form, replacing _atom_type_scat_versus_stol_list. It also allows scattering
# factors to be given for different wavelengths. The request for including
# more than one radiation type comes from Brian Toby who suggests that all the
# items that depend on radiation be brought into their own category to make it
# easier to describe multiradiation experiments without having to repeat
# values that do not depend on the scattering vector.
#
data_atom_type_scat_[]
_name '_atom_type_scat_[]'
_category category_overview
_type null
loop_
_example_detail
_example
'An example of a loop giving different types of scattering factors'
;
loop_
_atom_type_scat_factor_id
_atom_type_scat_factor_type_symbol
_atom_type_scat_factor_stol
_atom_type_scat_factor_scat_factor_real
_atom_type_scat_factor_scat_factor_imag
_atom_type_scat_factor_rad_type
1 S 0.0 16.0 0.2 X1
2 S 0.01 15.3 0.2 X1
3 S 0.03 14.8 0.2 X1
# data omitted for brevity
30 S 0.0 15.8 0.0 X2
31 S 0.01 15.0 0.0 X2
32 S 0.03 14.7 0.0 X2
# data omitted for brevity
60 V 0.0 23.0 ? X1
# data omitted for brevity
;
_definition
; This loop allows the scattering factors to be given explicitly as a function
of scattering angle (sin(theta)/(lambda)) for a variety of different
radiations.
;
#
# The following existing items would be moved into this category without
# change of name or description:
# _atom_type_scat_Cromer_Mann_*
# _atom_type_scat_dispersion_imag
# _atom_type_scat_dispersion_real
# _atom_type_scat_dispersion_source
# _atom_type_scat_length_neutron
# _atom_type_scat_source
# and _atom_type_scat_versus_stol_list would be retired. This change would be
# not strictly backwardly compatible, because earlier CIFs might be written
# with a mixture of _atom_type_* and _atom_type_scat_* items which is not
# allowed if they are in different categories. If this is a problem all
# new names could be created by substituting 'scatt' for 'scat'. The
# remaining items in the atom_type category are not dependent on the
# scattering vector.
#
# STATUS: open for discussion
data_atom_type_scat_factor_id
_name '_atom_type_scat_factor_id'
_category atom_type_scat
_type char
_type_conditions ?
_list yes
_list_mandatory yes
_related_item ?
_related_function ?
_definition
; An string that uniquely identifies each item in the atom_type_scat list.
;
# COMMENT: This is the mandatory list reference for this list.
# STATUS: Open for discussion
data_atom_type_scat_factor_type_symbol
_name '_atom_type_scat_factor_type_symbol'
_category atom_type_scat
_type char
_list yes
_list_reference '_atom_type_scat_factor_id'
_list_link_parent '_atom_site_type_symbol'
_definition
; A code used to identify the atom species representing this atom type. This
symbol may be composed of any characters except an underline with the
additional proviso that digits designate an oxidation state and must be
followed by a + or - character. It must match the _atom_site_type_symbol,
normally the chemical element symbol, which by default is the first one or two
characters of the _atom_site_label
;
# COMMENT:
# STATUS: Open for discussion
data_atom_type_scat_factor_rad_type
_name '_atom_type_scat_factor_rad_type'
_category atom_type_scat
_type char
_list yes
_list_reference '_atom_type_scat_factor_id'
_list_link_parent '_diffrn_radiation_wavelength_id'
_example
; X1, X2, CuK
;
_definition
; A flag indicating the radiation for which the scattering factor has the
given value. It must have the same value as one of the items listed under
_diffrn_radiation_wavelength_id.
;
# COMMENT: This provides a link to the diffraction experiment and the lists of
# structure factors.
# STATUS: Open for discussion
data_atom_type_scat_factor_scat_factor_imag
_name '_atom_type_scat_factor_scat_factor_imag'
_category atom_type_scat
_type numb
_list yes
_list_reference '_atom_type_scat_factor_id'
_units e
_units_detail electrons
_definition
; The imaginary part of the x-ray scattering factor at the given scattering
vector.
;
# COMMENT:
# STATUS: Open for discussion
data_atom_type_scat_factor_scat_factor_real
_name '_atom_type_scat_factor_scat_factor_real'
_category atom_type_scat
_type numb
_list yes
_list_reference '_atom_type_scat_factor_id'
_related_item '_atom_type_scat_versus_stol_list'
_related_function replace
_units e
_units_detail electrons
_definition
; The real part of the x-ray scattering factor at the given scattering
vector.
;
# COMMENT:
# STATUS: Open for discussion
data_atom_type_scat_factor_stol
_name _atom_type_scat_factor_stol
_category atom_type_scat
_type numb
_list yes
_list_reference '_atom_type_scat_factor_id'
_related_item '_atom_type_scat_versus_stol_list'
_related_function replace
_enumeration_range 0.0:
_units \%A^-1^
_units_detail Reciprocal angstroms
_definition
; Scattering vector expressed as sin(theta)/lambda at which the scattering
factor has the given value.
;
# COMMENT:
# STATUS: Open for discussion
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