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Review of coreCIF.dic (part 1)
- To: Multiple recipients of list <coredmg@iucr.org>
- Subject: Review of coreCIF.dic (part 1)
- From: "I. David Brown" <idbrown@mcmail.cis.mcmaster.ca>
- Date: Thu, 5 Sep 2002 20:46:37 +0100 (BST)
Dear Colleagues,
A month or so ago I circulated some proposed changes to the
coreCIF dictionary as part of the current major review. The items
included in that draft were those that I regarded as relatively
uncontroversial, selected from the full list of topics that we need to
consider, the intention being, that if we can first approve this more
straightforward set of proposals, we can then concentrate our efforts on
the more difficult issues.
The list of proposed straightforward changes was relatively long
consiting of over 50 items. Not surprisingly, given the time of year,
there was no response to my email. You all (I hope) filed it away
carefully before heading off on your summer holidays (except for our
friends down-under).
However, it is time to get down to serious business, so I propose
to focus the discussion on a small number of items at a time. Once each
group has been approved, we shall move on to the next.
Please respond to this email by using the 'reply to' address
without changing the subject heading. This will ensure that a proper
thread is provided for those reviewing the discussion on the web. Your
response is requested even if it is only to say that you approve, though I
will assume that if you do not respond it means that you are in full
agreement with the proposed changes. If you have reservations, even if
you cannot formulate your concerns clearly, please respond so that we can
put that item on hold for further discussion. No response means you
approve.
At this time I am bringing forward the first six items, those in
the Atoms_site and Atom_sites categories for discussion.
Because some of you will have deleted or misfiled the earlier
email, I enclose below the items that we are considering at this time (I
enclose the original document with the original list of contents but I
have deleted the 46 odd items that we are not considering at this time).
In order to move the process along, can you please reply by September 23.
Any items approved (or removed) by that time will be moved off the agenda
so that we can move on to the next group of items.
I look forward to your response.
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
*****************************************************
##################################################
#
# PROPOSED NEW DEFINITIONS FOR CIF_CORE_2.3.DIC
#
##################################################
#
# The following items are being proposed for inclusion in
# version 2.3 of the Core CIF dictionary. Each item is
# followed by a comment, explaining the rational for the
# proposal, and an indication of its status. As each item
# is approved, approval and the date of approval will be shown
# under the status. Any approved item will be included in the
# new version of the dictionary.
#
# This file contains the items that are relatively uncomplicated and
# that we should be able to approve without much trouble. Once these
# are out of the way we can then turn our attention to the more complex
# problems in the suggested agenda, viz:
# 1. Phase transition temperatures
# 2.1 to 2.4. Items dealing with disorder, rigid groups and those in the
# _atom_type category
# 5.2 Descriptions of peptide sequences. As CCDC will use internal names,
# this item is now deleted.
# 5.3 Description of crystal properties (may not be needed).
# 9.1 Twinning (awaiting the recommendations of a subcommittee)
# 9.4 definition of the diffraction orientation matrix
# 9.5 Flag for systematic absences
# 9.6 should the target be included in _diffrn_radiation rather than
# _*_source?
# 9.7 Standards for area detectors?
# 10.1 sample history and crystal growth
# 11.1 bond multiplicity
# 14.1 details of calculation of Fcalc
# 14.2 R factor for restrained refinement
# 14.3 Twinning (see 9.1)
# 17 Adoption of Space group category
#
# The following new datanames are proposed in this draft of the revisions to
# the core dictionary.
#
# ATOM SITE
# _atom_site_fract_ (modify)
# _atom_site_refinement_flags (replace with the following)
# _atom_site_refinement_flags_posn
# _atom_site_refinement_flags_adp
# _atom_site_refinement_flags_occupancy
# ATOM SITES
# _atom_sites_special_details
# CELL
# _cell_reciprocal_angle_alpha
# _cell_reciprocal_angle_beta
# _cell_reciprocal_angle_gamma
# _cell_formula_units_Z
# _cell_reciprocal_length_a
# _cell_reciprocal_length_b
# _cell_reciprocal_length_c
# CHEMICAL
# _chemical_melting_point_gt
# _chemical_melting_point_lt
# _chemical_properties_biological
# _chemical_properties_physical
# _chemical_temperature_decomposition
# _chemical_temperature_decomposition_gt
# _chemical_temperature_decomposition_lt
# _chemical_temperature_sublimation
# _chemical_temperature_sublimation_gt
# _chemical_temperature_sublimation_lt
# CITATION
# _citation_database_id_CSD
# DATABASE
# _database_code_depnum_ccdc_fiz
# _database_code_depnum_ccdc_journal
# _database_code_depnum_ccdc_archive
# _database_CSD_history
# DIFFRN
# _diffrn_ambient_pressure_gt
# _diffrn_ambient_pressure_lt
# _diffrn_ambient_temperature_gt
# _diffrn_ambient_temperature_lt
# DIFFRN_STANDARDS
# _diffrn_standards_decay_%_lt
# DIFFRN_REFLNS
# _diffrn_reflns_measured_faction_resolution_full
# _diffrn_reflns_measured_faction_resolution_max
# _diffrn_reflns_resolution_full
# _diffrn_reflns_resolution_max
# EXPTL_CRYSTAL
# _exptl_crystal_colour (modification)
# _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
# PUBL
# _publ_contact_author_id_iucr
# PULB_AUTHOR
# _publ_author_id_iucr
# REFINE
# _refine_ls_extinction_coef
# _refine_ls_extinction_coef_Zach
# _refine_ls_extinction_coef_Becker-Coppens_1
# _refine_ls_extinction_coef_Becker-Coppens_2
# _refine_ls_extinction_BC_type
# _refine_ls_extinction_expression
# _refine_ls_extinction_method
# _refine_ls_shift/su_max_lt
# _refine_ls_shift/su_mean_lt
#
##################################################
##################################################
#
# ATOM SITE
#
##################################################
data_atom_site_fract_
loop_ _name '_atom_site_fract_x'
'_atom_site_fract_y'
'_atom_site_fract_z'
_category atom_site
_type numb
_type_conditions esd
_related_item '_atom_site_Cartn_'
_related_function alternate
_list yes
_list_reference '_atom_site_label'
# _enumeration_default 0.0
_definition
; Atom site coordinates as fractions of the _cell_length_ values.
;
# COMMENT: The default should be deleted since it makes no sense. If the
# coordinates are defaulted it is, presumably, because they are not known, not
# because the atom is at the origin.
# STATUS: Open for discussion
#data_atom_site_refinement_flags
# _name '_atom_site_refinement_flags'
# _category atom_site
# _type char
# _list yes
# _list_reference '_atom_site_label'
# loop_ _enumeration
# _enumeration_detail . 'no refinement constraints'
# S 'special position constraint on site'
# G 'rigid group refinement of site'
# R 'riding-atom site attached to non-riding atom'
# D 'distance or angle restraint on site'
# T 'thermal displacement constraints'
# U 'Uiso or Uij restraint (rigid bond)'
# P 'partial occupancy constraint'
# _definition
#; A concatenated series of single-letter codes which indicate the
# refinement restraints or constraints applied to this site.
#;
# COMMENT: The proposal is to replace this item by the following three. The
# problem with the current definition is that it requires the character field
# to be parsed since any of the seven flags may appear in any order. The
# replacement items define unique flags for each possibility.
# STATUS: Open for discussion
data_atom_site_refinement_flags_posn
_name '_atom_site_refinement_flags_posn'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
loop_ _enumeration
_enumeration_detail . 'no refinement constraints'
D 'distance or angle restraint on site'
G 'rigid group refinement of site'
R 'riding-atom site attached to non-riding atom'
S 'special position constraint on site'
DG 'combination of the above constraints'
DR 'combination of the above constraints'
DS 'combination of the above constraints'
GR 'combination of the above constraints'
GS 'combination of the above constraints'
RS 'combination of the above constraints'
DGR 'combination of the above constraints'
DGS 'combination of the above constraints'
DRS 'combination of the above constraints'
GRS 'combination of the above constraints'
DGRS 'combination of the above constraints'
_definition
; A code which indicates the refinement restraints or constraints
applied to the positional coordinates of this site.
;
# COMMENT: Are some of these flags mutually exclusive, allowing the list to be
# shortened?
data_atom_site_refinement_flags_adp
_name '_atom_site_refinement_flags_adp'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
loop_ _enumeration
_enumeration_detail . 'no refinement constraints'
T 'atomic displacement constraints'
U 'Uiso or Uij restraint (rigid bond)'
TU 'Both constraints applied'
_definition
; A code which indicates the refinement restraints or constraints
applied to this atomic displacement parameters of this site.
;
# COMMENT: Are these enumeration details clear? What is the difference
# between these two flags? Can both apply at the same time?
data_atom_site_refinement_flags_occupancy
_name '_atom_site_refinement_flags_occupancy'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
loop_ _enumeration
_enumeration_detail . 'no refinement constraints'
P 'partial occupancy constraint'
_definition
; A code which indicates that refinement restraints or
constraints were applied to the occupancy of this site.
;
##################################################
#
# ATOM SITES
#
##################################################
data_atom_sites_special_details
_name '_atom_sites_special_details'
_category atom_sites
_type char
_definition
; Additional information about the atomic coordinates not coded
elsewhere in the CIF.
;
# COMMENT: This could be useful in transcribing comments in databases.
# STATUS: Open for discussion
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