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coreCIF.dic-2.4 Discussion List #8
- To: Distribution list of the IUCr COMCIFS Core Dictionary Maintenance Group <[email protected]>
- Subject: coreCIF.dic-2.4 Discussion List #8
- From: David Brown <[email protected]>
- Date: Fri, 21 Apr 2006 14:17:09 -0400
April 21, 2006
Dear members of the coreCIF Dictionary Maintenance Group
####################################################################
#
# PLEASE RESPOND BY 2006-05-15. IF THIS IS INSUFFICIENT TIME LET ME
# KNOW AND I WILL EXTEND THE DEADLINE.
#
# PLEASE DO NOT BE DISCOURAGED BY THE LENGTH OF THIS MESSAGE, BUT READ
# THE INTRODUCTION FIRST.
#
####################################################################
INTRODUCTION
I apologize for the lack of activity in this discussion over the last
few months. This was not entirely laziness on my part. Around the
beginning of last summer it became clear that some important decisions
were going to have to be made about the future directions of CIF and
there seemed to be no points in working on details until we knew which
way the project was headed.
The meetings held at the IUCr Congress in Florence produced a remarkable
consensus about the future of CIF and now that we have a general idea of
the future directions it is time to go back and finish off the
modifications needed to the coreCIF dictionary.
First I will summarize the decisions taken in Florence as these will
have a bearing on the work of the core Dictionary Maintenance Group. It
was agreed that we should define a new Dictionary Definition Language,
DDL3, based on the prototype starDDL first demonstrated by Syd Hall at
the Glasgow IUCr Congress. For convenience I will refer to the CIF
dictionaries prepared with the Dictionary Definition Languages DDL1,
DDL2 and DDL3 as CIF1 (coreCIF.dic etc.), CIF2 (mmCIF.dic etc.) and CIF3
dictionaries respectively, and the corresponding CIFs as CIF1, CIF2 and
CIF3. Programs designed to work with CIF3 will be able to read all the
archives written in CIF1 and CIF2, but they will also be able to handle
several enhancements available in CIF3, such as the ability to define
vectors and matrices. CIF3 dictionaries will be based on a more
hierarchical arrangement of categories designed to simplify the
maintenance of the dictionaries, and they will include 'methods', i.e.,
they will be able to interpret algorithms or equations contained in the
dictionary in order to calculate the value of an item that is not
present in the CIF. In effect, methods are a machine readable definition.
There is much work to be done before DDL3 is ready for launching because
the dictionaries will have to be converted and extended, and software
will need to be prepared. CIF1 and CIF2 dictionaries will continue in
use until users, convinced by the superiority of CIF3, have voluntarily
converted. One consequence of the hierarchical arrangement of concepts
is that the suite of CIF dictionaries will likely be reorganized
requiring a corresponding reorganization of the Dictionary Maintenance
Groups. Even though the members present in Florence wanted to see CIF3
introduced as soon as possible, it will take a minimum of two years
before a core dictionary and software are ready for beta testing.
Even with the new initiative the CIF1 core dictionary will be around for
some years to come. Therefore the core Dictionary Maintenance Group
still has work to do. However, some of the proposals we have been
discussing, e.g., adding chemical information to identify molecules
etc., will be deferred to CIF3, but in the meantime there are many
changes that we still need to make in CIF1. These are treated in this
email.
Best wishes
David Brown
**********************
Proposed changes to the coreCIF1 dictionary
Earlier rounds of changes have now been incorporated in coreCIF.dic
version 2.3, the version that appears in International Tables vol. G.
Some items that had been approved for this version were pulled at the
last minute as serious objections were raised. Some of these were
included in discussion #7, and as I received no comments on this list,
all those items for which approval was recommended have now been moved
to the draft coreCIF.dic version 2.4 (you will get a chance to see these
again before we submit them to COMCIFS for final approval).
This discussion, #8, contains four sections. Section A consists of
items which I recommend we drop. Section B consists of items that are
ready for approval. Section C contains items needing further discussion
and Section D contains a number of miscellaneous comments.
####################################
####################################
#
# A. ITEMS THAT PROBABLY WE CAN DROP
#
####################################
####################################
#
# 1. DIFFRN_REFLN_STATUS
#
# 2. CHEMICAL FORMULA
#
###################################
#
# These items were proposed for coreCIF.dic 2.3 but were withdrawn
# because of problems. As the problems have not gone away
# I will drop these items unless anyone objects.
#
# RECOMMENDATION: These items be dropped.
#
####################################
#
# 1. DIFFRN_REFLN_STATUS
#
data_diffrn_refln_status
_name '_diffrn_refln_status'
loop_
_enumeration
_enumeration_detail
incl 'Reflection expected to have non-zero intensity'
sysabs 'Reflection considered to be systematically absent'
_example
_definition
; A flag indicating whether a reflection was assumed to be
systematically absent during the measurement of the diffraction
intensities.
;
# COMMENT: The purpose of this item was to allow reflection that are
believed
# to be systematically absent to be flagged at the time they were measured.
# However as HDF points out, in order to know which reflections are
# absent one must know the space group and this is only chosen later in the
# process. For this flag to be meaningful, a tentative space group
would have
# to be given in the CIF, but this would be meaningless (and confusing)
if it
# were different from the one finally adopted. There is a way of marking
# systematically absent reflections in the refln category calculated
after the
# structure has been solved and the space group is known.
#
########################################
#
# 2. CHEMICAL FORMULA
#
# In another discussion group Peter Murray-Rust suggested that the
# chemical_formula should indicate how the formula was obtained. He thought
# that _chemical_formula_sum was inadequate because it does not indicate
# whether the formula was derived from the crystal structure or
analytically.
# He suggested that we should define _chemical_formula_sum_calc and
# _chemical_formula_sum_meas.
#
# HDF writes
# ----------
# In my opinion, further discussion on this point should be pushed off
to the
# coreDMG or coreCIFchem list.
#
# Peter has a good point with regard to _chemical_formula[] that should be
# borne in mind in relation to the work of the "group" coreCIFchem. The
names
# need to indicate as precisely and succinctly as possible the source of the
# information.
#
# However I must say that I think that particularly bad in this respect are
# suffixes such as _meas and _calc because more or less everything we deal
# with comes from some sort of a measurement and has to be calculated to a
# greater or lesser extent. Much better are _analytical or _massspectrometry
# or _xraydiffraction.
#
# IDB comments
# ------------
# The coreCIFchem group, charged with providing a chemical description
of the
# contents of a crystal, is currently inactive pending the introduction of
# CIF3.
# _chemical_formula_sum (and _moiety, _structural etc.) must agree
# exactly with the refined model presented in the atom_site loop. so
they are
# determined from the structure determination. They might
# therefore be considered to correspond to PMR's _calc or HDF's
# _xraydiffraction. There is a _chemical_formula_analytical which is
designed
# for information about the composition derived using a non-crystallographic
# method. There is something to be said for adding other terms like
_massspec
# or _xrf (x-ray fluorescence), but these could wait until there is a
demand.
# _*_analytical is rarely used.
#
####################################
######################################
######################################
#
# B. ITEMS THAT ARE READY FOR APPROVAL
#
#--------------------------------------
#
# 3. GEOM_*_SITE_SYMMETRY (Largely housekeeping)
#
# 4. DISTRIBUTED ELECTRON DENSITY (Discussed earlier)
#
#
######################################
######################################
#
# These are items that have either been discussed before or are in the
nature
# of housekeeping. If there are no objections raised, these will be
accepted
# for incorporation into coreCIF.dic version 2.4
#
#####################################
#
# 3. GEOM_*_SITE_SYMMETRY Revisited
# Changes to this item were approved in discussion #7 but we need to revisit
# this item.
#
#####################################
#
# EXPLANATION
# In Discussion #7 we approved splitting geom_*_site_symmetry into four
items
# (item #1 in our approved list):
#
# _geom_*_site_symmetry_symop
# _geom_*_site_symmetry_trans_a
# _geom_*_site_symmetry_trans_b
# _geom_*_site_symmetry_trans_c
#
# The reason for this change was so as not to limit the distance over
which a
# symmetry-related atom could be addressed. However, since the vector
format
# in DDL3 provides a more elegant solution to this problem which in any
# case is not of high priority, it is best to leave this to CIF3.
# Therefore our earlier approval of these items should be withdrawn
#
# There is, however, a more immediate problem we need to address.
#
# In the first version of the core dictionary default values were introduced
# for a number of items, but some of these made little sense, e.g., a
default
# of 0 for h, k and l. We have gradually been removing these meaningless
# defaults, but in the case of _geom_*_site_symmetry a default has
always been
# assumed (on the basis of an example given in dictionary) even though no
# default is given in the dictionary definition.
# Most currently generated CIFs use a period to
# indicate that this item defaults to 1_555, i.e., the coordinates given in
# the atom_site list are not transformed. In the proposed change this
default
# is made explicit.
#
# Related to this is the fact that there is currently no requirement in the
# dictionary that symop 1 be the identity operation.
# We therefore need to add a note to the definitions of several items
# that the _*_id value of the identity operation should
# be 1.
#
#
#
# PROPOSAL
# 1. Drop the recently approved items
# _geom_*_site_symmetry_symop
# _geom_*_site_symmetry_trans_a
# _geom_*_site_symmetry_trans_b
# _geom_*_site_symmetry_trans_c
#
# 2. Add to _space_group_symop_id and _symmetry_equiv_pos_site_id
# _enumeration_default 1
#
# 3. Add to _symmetry_equiv_pos_as_xyz
# _enumeration_default x,y,z
#
# 4. Add the following sentence to the definitions of
# _space_group_symop_operation_xyz, _space_group_symop_id,
# _symmetry_equiv_pos_as_xyz and _symmetry_equiv_pos_site_id:
#
#; In order for the defaults to work correctly, the
identity
# operation should have _space_group_symop_id or
# _symmetry_equiv_pos_site_id set to 1, and
# _space_group_symop_operation_xyz or
# _symmetry_equiv_pos_as_xyz set to x,y,z,
# i.e., the operation labelled 1 should be the identity
# operation.
#;
#
# RECOMMENDATION: That this item be approved.
#
####################################
#
# 4. DISTRIBUTED ATOMIC DENSITY Ready for approval
#
#####################################
#
# STATUS: Ready for approval
#
# RECOMMENDATION: The following items be approved
#
# INTRODUCTION
#
# The following items which were included in the previous discussion are
based
# on a request from David Watkin.
# They are intended to describe atoms that are disordered or moving so that
# their atomic density is assumed to be distributed over a simple geometric
# shape such as a ring as might arise from a rotating group such as a
# trifluooromethyl group or a cyclopentadiene molecule.
#
# Various possible shapes are defined - ring, spherical shell,
# cylindrical shell, etc. The atoms that form the ring or shell are listed
# with dummy coordinates in the atom_site loop. This is necessary to allow
# the composition of the crystal to be calculated.
# The dummy atoms are flagged with an identifier
# that links them to a new category giving details of the shape of the
# distribution, thus allowing, e.g., the scattering density to be
calculated.
# This requires the introduction of an _atom_site_distributed_density_id
item
# in the atom_site category, and the definition of a new distributed_density
# category.
#
# David Watkins is currently adapting CRYSTALS to provide a CIF output for
# distributed density and for this purpose he is defining a few extra local
# 'Oxford' datanames: specifically an _atom_site_occupancy that may take
# values greater than 1.0 (not permitted in _atom_site_occupancy) and
items to
# define the directions of lines, rings, etc. in terms of Euler angles based
# on the choice of orthogonal axes assumed by CRYSTALS. The method of
# defining the direction (based on reciprocal space coordinates) given
here is
# independent of any arbitrary convention.
#
# I apologize for the length of this item, but we have seem it all before.
#
#################
#
# A new item for the ATOM_SITE category
#
#################
#
data__atom_site_distributed_density_id
_name '_atom_site_distributed_density_id'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_list_mandatory no
_link_parent '_distributed_density_id'
_example ?
_definition
; An identifier that links the atom defined by _atom_site_label
with the distributed density of this atom defined in the
distributed_density category.
Note that all the atoms that give rise to a particular
distributed density, e.g., a ring, should be included in the
atom_site list, even when they, or the centroid of the
distribution, lie on a special position.
That is, the crystallographic site symmetry of the
distribution
is not used to
generate the full distributed density shape from the
crystallographic asymmetric portion.
The value of _atom_site_symmetry_multiplicity should be
chosen
so that for each of the atoms in the atom_site list
_atom_site_occupancy multiplied by
_atom_site_symmetry_multiplicity is equal to its contribution
to the _chemical_formula_sum multiplied by
_cell_formula_units_Z.
;
#
#
##########################
#
# New Category DISTRIBUTED DENSITY
#
##########################
#
data_distributed_density_[]
_name '_distributed_density_[]'
_category category_overview
_type null
_definition
; Items in the distributed_density category describe the
geometric arrangement of an atom or atoms when they are
distributed uniformly over a line or surface such as a ring,
cylindrical shell or spherical shell, the line or surface
being
given a thickness through the application of an atomic
displacement parameter.
;
loop_ _example_detail
_example
;
This example is fictitious (and chemically implausible) but it is
designed to illustrate how a complex system of distributed density can
be recorded. In this example pentamethyl cyclopentadiene (Cp*) and
borazole occupy the same location in the crystal in the ratio 5:1. The
atoms of the borazole ring are fixed as are three quarters of the atoms
in the Cp* ring, but the remaining quarter of the Cp* molecules are
freely rotating around the cylindrical Cp* axis. The rotating Cp*
molecules give rise to two concentric rings of density, one from the
atoms in the ring and the other from the methyl groups (hydrogen atoms
are ignored). On top of these rings lie the atoms of the fixed Cp*
molecules. The atoms of the borazole molecule also lie over the inner
Cp* ring. Full details of the chemical composition are given in the
atom_site loop together with the positions of the fixed atoms.
The coordinates of the atoms that give rise to the distributed ring of
density are set to '.', meaning that they have no significance as the
atoms are dummy atoms included to give the correct composition providing
that _atom_site_occupancy and _atom_site_symmetry_multiplicity are given.
The composition defined in the atom_site loop is linked to the
distributed_density loop through the parent-child identifiers, 'an1' and
'an2' (for annulus 1 and 2).
The one quarter of the Cp* molecules that are rotating have the occupation
number of 0.208 = 5/6 (the total occupancy of the Cp*) x 1/4 (the portion
rotating) = 5/24. The three quarters that are in fixed positions have
the occupation number of 0.625 = 5/6 x 3/4 = 15/24 .
;
;loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_occupancy
_atom_site_symmetry_multiplicity
_atom_site_adp_type
_atom_site_distributed_density_id
_atom_site_calc_flag
#
# Inner ring of cyclopentadiene carbon atoms and borazole
C1 C -0.1362(8) -0.0974(8) -0.3116(10) 0.0662(18) 0.625(1) 4 Uiso . d
C2 C -0.1060(8) -0.2165(8) -0.1837(10) 0.071(2) 0.625(1) 4 Uiso . d
C3 C -0.1774(9) -0.1939(9) -0.0820(11) 0.082(2) 0.625(1) 4 Uiso . d
C4 C -0.2529(9) -0.0561(9) -0.1479(12) 0.084(2) 0.625(1) 4 Uiso . d
C5 C -0.2261(8) -0.0002(8) -0.2891(10) 0.072(2) 0.625(1) 4 Uiso . d
C1a C . . . . 0.208(1) 4 .
an1 dum
C2a C . . . . 0.208(1) 4 .
an1 dum
C3a C . . . . 0.208(1) 4 .
an1 dum
C4a C . . . . 0.208(1) 4 .
an1 dum
C5a C . . . . 0.208(1) 4 .
an1 dum
N1 N -0.1375(8) -0.0968(8) -0.3201(10) 0.065(2) 0.167(1) 4 Usso . d
B1 B -0.1002(8) -0.2265(8) -0.1728(10) 0.071(2) 0.167(1) 4 Uiso . d
N2 N -0.1402(8) -0.1034(8) -0.0765(10) 0.076(2) 0.167(1) 4 Uiso . d
B2 B -0.2370(9) -0.0364(9) -0.1832(10) 0.085(2) 0.167(1) 4 Uiso . d
N3 N -0.2893(8) 0.0034(8) -0.3621(10) 0.062(2) 0.167(1) 4 Uiso . d
B3 B -0.2246(9) -0.0452(9) -0.3004(11) 0.073(2) 0.167(1) 4 Uiso . d
# Outer ring of methyl groups
C11 C -0.0951 -0.0733 -0.4330 0.1901 0.625(1) 4 Uani . d
C12 C -0.0272 -0.3236 -0.1750 0.1990 0.625(1) 4 Uani . d
C13 C -0.1719 -0.2833 0.0404 0.2483 0.625(1) 4 Uani . d
C14 C -0.3291 -0.0080 -0.0844 0.2450 0.625(1) 4 Uani . d
C15 C -0.2817 0.1218 -0.3770 0.2219 0.625(1) 4 Uani . d
C11a C . . . . 0.208(1) 4 .
an2 dum
C12a C . . . . 0.208(1) 4 .
an2 dum
C13a C . . . . 0.208(1) 4 .
an2 dum
C14a C . . . . 0.208(1) 4 .
an2 dum
C15a C . . . . 0.208(1) 4 .
an2 dum
# Details of the two rings of distributed density are given in the following
# loop.
loop_
_distributed_density_id
_distributed_density_shape
_distributed_density_position_x
_distributed_density_position_y
_distributed_density_position_z
_distributed_density_radius
_distributed_density_direction_h
_distributed_density_direction_k
_distributed_density_direction_l
_distributed_density_Uiso
_distributed_density_symmetry_multiplicity
an1 ring -0.1810(8) -0.1133(8) -0.2058(8)
1.198(6) 1.35(2) 0.07(2) -0.45(2) 0.052(2) 4
an2 ring -0.1873(14) -0.1156(14) -0.2210(2)
2.626(6) 1.30(2) 0.10(2) -0.40(2) 0.131(3) 4
;
data_distributed_density_details
_name '_distributed_density_details'
_category distributed_density
_type char
_list both
_list_reference '_distributed_density_id'
_example
; The distribution was modelled using a disk of
density of the given radius.
;
_definition
; Information about the distribution of density not
given in other items.
;
data_distributed_density_direction_
loop_ _name
'_distributed_density_direction_h'
'_distributed_density_direction_k'
'_distributed_density_direction_l'
_category distributed_density
_type numb
_type_conditions esd
_list both
_list_reference '_distributed_density_id'
_units rlu
_units_detail reciprocal lattice units
_example ?
_definition
; The (covariant) components on a reciprocal-lattice basis of a
vector of
arbitrary length used to indicate the direction of the unique axis of
the distribution, e.g., the axis of a cylindrical shell or the normal
to the plane of a ring.
;
data__distributed_density_id
_name '_distributed_density_id'
_category distributed_density
_type char
_list both
_list_reference '_distributed_density_id'
_list_mandatory yes
_link_child '_atom_site_distributed_density_id'
_example ?
_definition An identifier that links the atom defined by
_atom_site_label with a distributed density defined in
the distributed_density category.
;
#
data__distributed_density_length
_name '_distributed_density_length'
_category distributed_density
_type numb
_type_conditions esd
_list both
_list_reference '_distributed_density_id'
_enumeration_range 0.0:
_units A
_units_detail Angstrom units
_example ?
_definition
; The length of the line or cylindrical shell of distributed
density in Angstrom units.
;
#
data__distributed_density_position_
loop_ _name
'_distributed_density_position_x'
'_distributed_density_position_y'
'_distributed_density_position_z'
_category distributed_density
_type numb
_type_conditions esd
_list both
_list_reference '_distributed_density_id'
_example ?
_definition
; The position of the centroid of the distributed density in
fractions of the unit cell values.
;
#
data__distributed_density_radius
_name '_distributed_density_radius'
_category distributed_density
_type numb
_type_conditions esd
_list both
_list_reference '_distributed_density_id'
_enumeration_range 0.0:
_units A
_units_detail Angstrom units
_example ?
_definition
; The radius of the ring, or of the cylindrical or spherical
shell, of distributed density in Angstrom units.
;
#
data__distributed_density_shape
_name '_distributed_density_shape'
_category 'distributed_density
_type char
_list both
_list_reference '_distributed_density_id'
loop_
_enumeration
_enumeration_detals
line 'line segment'
infline 'an infinite line running through the crystal'
ring 'a circular ring'
cylshell 'cylindrical shell of finite length'
infcylshell 'cylindrical shell running through the crystal'
sphereshell 'spherical shell'
other 'Give details in _distributed_density_details'
_definition
; A flag that indicates the shape of the distributed density.
The lines and ring are one dimensional distributions of
atoms and the cylindrical shell and spherical shell are two
dimensional distributions.
In each case the root-mean-square thickness of the
distribution
is given by the atomic displacement parameter defined in
_distributed_density_Uiso.
;
data__distributed_density_symmetry_multiplicity
_name '_distributed_density_symmetry_multiplicity'
_category distributed_density
_type numb
_list both
_list_reference '_distributed_density_id'
_enumeration_range 1:192
_example ?
_definition
; The number of images of the centroid of the distributed
density
that the space group symmetry generates in the unit cell
reported in the cell category. It is the number that
appears in International Tables for Crystallography Vol A for
the Wyckoff position occupied by the centroid.
In this treatment the symmetry of the distribution itself is
ignored, including any operations of its point group that are
part of the crystallographic site symmetry of the
centroid.
All the atoms that give rise to the distributed density
should
therefore be listed in the atom_site category even if
they, or
the centroid of the distribution, lie on crystallographic
special positions.
E.g., if the distribution is a ring and the centroid of the
ring lies on a crystallographic mirror plane, all the
atoms in
ring are listed if the ring lies either in or
perpendicular to
the mirror plane since the mirror image of the ring lies over
the ring itself.
If the ring is at some arbitrary angle to the mirror
plane, the
mirror generates a second ring and both rings should be
described independently.
However, because both rings cannot be simultaneously
occupied,
the occupation numbers given in the atom_site category must
have a value equal to or less than 0.5.
;
#
data__distributed_density_Uiso
_name '_distributed_density_Uiso'
_category distributed_density
_type numb
_type_conditions esd
_list both
_list_reference '_distributed_density_id'
_enumeration_range 0.0:
_units A^2^
_units_detail 'Angstrom units squared'
_example 0.018(3)
_definition
; The factor exp(-Ux^-2^)is applied to all parts of the
distribution, where U = _distributed_density_uiso and x is the distance
from the ideal 1- or 2- dimensional shape. This emulates the effects of
thermal motion or static displacement from the ideal positions described
in this category and has the effect of converting the simple 1- or
2-dimensional geometric shapes into 3-dimensional objects of mean square
thickness U.
;
#
########################################
########################################
#
# C. ITEMS REQUIRING FURTHER DISCUSSION
#
########################################
########################################
#
# 5. GEOM_BOND Open for discussion
#
# 6. _EXPTL_ABSORPT_CORRECTION_T_max and T_min Open for discussion
#
# 7. REFINE_ELECTRON_DENSITY Open for discussion
#
# 8. _ATOM_SITE_REFINMENT_FLAG_ADP Open for discussion
#
# 9. _ATOM_SITES_SOLUTION_* Open for discussion
#
# 10. _CHEMICAL_ENANTIOEXCESS_BULK_* Open for discussion
#
# 11. _PUBL_SECTION_KEYWORDS Open for discussion
#
# 12. DIMENSIONLESS UNITS Open for discussion
#
##########################################
#
# 5. GEOM_BOND
#
##########################################
#
# COMMENT: In high symmetry structures when many bonds are related by
symmetry
# it is not necessary to list all the bonds in the environment of the first
# named atom. Some users may wish to give only the symmetry independent
# distances and a multiplier to indicate how many such bonds are found
in the
# atomic environment.
#
data_geom_bond_multiplicity
_name '_geom_bond_multiplicity'
_category geom_bond
_type numb
_type_conditions
_list yes
_list_reference '_geom_bond_atom_site_label_'
_enumeration_range 0:
_definition
; The number of times the given bond appears in the environment of
the atoms labelled _geom_bond_atom_site_label_1.
;
# STATUS: Open for discussion
###########################################
#
# 6. EXPTL_ABSORPT_CORRECTION_T_max and T_min
#
###########################################
#
# The current definition of these items is:
#
# The maximum and minimum transmission factors for the crystal
# and radiation. These factors are also referred to as the
# absorption correction A or 1/A*.
#
# but there have been a variety of different interpretations as to what this
# means, viz:
#
# 1. These values are the transmission factors that were used in correcting
# the diffraction intensities for absorption. (Acta Cryst. has adopted this
# interpretation.)
#
# 2. These are the true transmission factors, whether or not any correction
# was made for absorption. They are shown to give an indication of the
# importance of absorption in this specimen.
#
# 3. These corrections apply to the crystal alone and not the specimen mount
# (e.g., the capillary).
#
# 4. These corrections apply to the crystal and specimen mount (including
# mother liquor and container). In some experiments (e.g., in a diamond
anvil
# high pressure experiment) the container may absorb more strongly than the
# specimen.
#
# And how should these be interpreted in the case of multiple wavelengths
# where the transmission factors are not constant?
#
# These uncertainties should be resolved. Maybe we need more than one
set of
# transmission factors. Your suggestions would be welcome.
#
# Relevant to this discussion are comment received from Ross Angel who is
# is writing a program for reporting high-pressure results as CIF.
#
# RA writes:
# ----------
# The most important issues with respect to high-pressure data concern data
# corrections and how to describe them in the cif. At least the following
# issues would need to be addressed:
#
# 1) A flag to tell cif checkers that completeness is not expected
because of
# restrictions by the sample conditioning device.
#
# 2) Definition of whether the terms _exptl_absorpt_correction_T_max and
T_min
# apply to the total correction to an intensity, or just the correction from
# the crystal.
#
# 3) A way to document the corrections for the absorption and shadowing
by the
# pressure cell
#
# 4) A way to describe the crystal faces in an x-y-z coordinate system
instead
# of hkl and d. The crystal faces approach is not appropriate for many
# high-pressure devices.
#
# The problem with items 3 and 4 is that they will differ from one lab to
# another. What I have done is to put all of this information into
# "_exptl_absorpt_process_details" and "_exptl_crystal_description " as
# follows:
#
_exptl_absorpt_process_details
;
Gaussian integration over a grid
of 16 x 8 x 16 points = 2048 total grid points
Based upon method of Burnham (1966)
Data corrected for diamond-anvil cell absorption
Note that exptl_absorpt_correction_tmin and _tmax
the total correction factors applied to the intensities
The individual factors are:
range of dac transmission factors (min-max) 0.703
0.980
range of gasket transmission (min-max) 0.992
1.000
range of P media transmission (min-max) 1.000 1.000
DAC transmission function with sum(mu*t) for anvil 1: 0.607 anvil 2:
0.607
Gasket shadowing corrections were made based upon
Gasket thickness = 114.0 microns, radius = 140.0 microns
Gasket absorption coeff = 30.00 mm-1
REFLECTION WAS CONSIDERED TOTALLY OBSCURED IF
FRACTION CRYSTAL ILLUMINATED WAS LESS THAN 0.20
Non-absorbing pressure medium
;
_exptl_crystal_preparation 'mounted in a diamond-anvil cell '
_exptl_crystal_description
;
crystal was described in terms of coordinates of corners on the
orthogonal phi-axis coordinate system of Busing and Levy (1967) (i.e.,
+Y along beam, +Z up at circles zero, +X to make right-handed set)
with origin at the centre of the face of the incident-beam anvil loop
is over x, y, z (mm)
-0.044000 0.000000 0.061000
0.073000 0.000000 0.032000
-0.069000 0.000000 -0.032000
0.048000 0.000000 -0.060000
-0.044000 0.060000 0.061000
0.073000 0.060000 0.032000
-0.069000 0.060000 -0.032000
0.048000 0.060000 -0.060000
;
#
# [IDB: See the note in Section D below regarding choice of axis systems in
# CIF. The choice adopted here is different.]
#
# STATUS: Open for discussion.
#
##########################################
#
# 7. REFINE_ELECTRON_DENSITY
#
##########################################
#
# COMMENT: The following items form a new category giving a list of peaks
# in the electron density.
# This has been requested by a user as a useful adjunct to the other refine
# items.
#
# This does, however, raise the question of whether there might be a greater
# need for other peak functions such as peaks in the Patterson function
or in
# the difference electron density.
#
# Without any further information supplied elsewhere by the user,
# one would assume that these peaks are those found in the final electron
# density map, but the examples given below suggest that it might be a
density
# map produced much earlier in the structure determination process.
# Since the final structure is fully described by the list of occupied
# atom_sites, it is not clear that knowing the positions and heights of the
# peaks in the final electron density map is of much value except in the
rare
# case where a number of peaks do not occur at atom sites.
#
# Is the name correct or should we use a more general name
# such as _refine_scattering_density? If this is generalized to include
# neutron diffraction results, _*_peak might presumably be negative.
#
data_refine_electron_density_[]
_name refine_electron_density
_category null
_type category_overview
_example
; loop_
_refine_electron_density_id
_refine_electron_density_position_x
_refine_electron_density_position_y
_refine_electron_density_position_z
_refine_electron_density_peak
_refine_electron_density_details
1 0.0743 0.3568 0.4215 45.6 'probably Mo'
2 0.7358 0.2987 0.8932 43.2 'probably Mo'
3 0.8657 0.4518 -0.0654 25.8 ?
;
_definition
; This is a category in which the peak positions and heights in
the experimental electron density map can be reported.
;
# STATUS: Open for discussion
data_refine_electron_density_details
_name '_refine_electron_density_details'
_category refine_electron_density
_type char
_list yes
_list_reference '_refine_electron_density_details
loop_ _example 'Probably Mo'
'Uncertain peak'
'Broad diffuse peak'
_definition
; A description of the electron density peak
;
data_refine_electron_density_id
_name '_refine_electron_density_id'
_category refine_electron_density
_type char
_list yes
_example ?
_definition
; A code identifying this particular electron density peak
;
data_refine_electron_density_peak
_name '_refine_electron_density_peak'
_category refine_electron_density
_type numb
_list yes
_list_reference '_refine_electron_density_id'
_units e.A-3
_units_detail 'electrons per cubic angstrom'
_example ?
_definition
; The measured electron density at the given peak position.
;
data_refine_electron_density_position_
loop_
_name _refine_electron_density_position_x
_refine_electron_density_position_y
_refine_electron_density_position_z
_category refine_electron_density
_type char
_list yes
_list_reference _refine_electron_density_id
_example ?
_definition
; The positional coordinates in fractions of the unit cell at
which the electron density peak occurs.
;
# STATUS: Open for discussion
#
########################################
#
# 8. _ATOM_SITE_REFINMENT_FLAG_ADP
#
########################################
#
# Curt Haltiwanger suggests that we need to extend the enumeration list for
# this item. He writes:
#
# There are at least three common restraints for adp's
#
# 1. 'rigid bond' [SHELXL - DELU] restraint - i.e. the components of the
# adp in the direction of the bond are restrained to have similar numerical
# values
#
# 2. 'near neighbor' (My term) [SHELXL - SIMU] restraint - Atoms closer
# than a specified distance are restrained to have the same Uij components.
#
# 3. 'approximate isotropic' (My term) [SHELXL - ISOR] restraint - atoms
# are restrained so that their Uij components approximate to isotropic
# behavior
#
# The enumeration detail should reflect these possibilities and those in
other
# refinement packages.
#
# In addition, SHELXL can has the provision for several atoms to have
exactly
# the same adp's or some multiplier times the adp. These would also be a
# candidate for enumeration. I have no knowledge of the restraints and
# constraints used in other programs.
#
# [IDB: COMMENT: There is confusion between the meaning of 'constraint' and
# 'restraint'. A 'constrained parameter' is one that is not refined.
It may
# be reset between refinements, e.g., to be equal to one of the refined
# parameters, and so may change as the refinement progresses, but it is
not a
# variable in the least squares calculation. A 'restraint' is a target
value
# for some structure dependent variable (not one that is being
# refined) that is added to the target list of observed structure
factors and
# is treated as an observation, suitably weighted. I believe that Curt is
# referring here to constraints, not restraints.
#
# The list of flags in the current dictionary is:
#
# . No constraints
# T Special position constraints on ADPs
# U Uiso or Uij restraint (sic) (rigid bond)
# TU Both constraints applied.]
#
# CH continues:
# So
# S 'special-position constraints on atomic displacement parameters'
# [this should be T, IDB]
# R
#; adp in the direction of connecting bond are restrained to similar
# (rigid bond)
#;
# N 'adp of nearby atoms are restrained to have similar Uij's
# I 'adp restrained to approximate isotropic behavior'
# E 'adp exactly tied to adp of another atom'
# M 'adp based on multiplication factor of the adp of another atom'
# SR 'combination of the above constraints'
# SN 'combination of the above constraints'
# SI 'combination of the above constraints'
# SE 'combination of the above constraints'
# etc
#
# Alternatively remove rigid bond from the definition
# U 'Uiso or Uij restraint'
# or add other possibilities
# U 'Uiso or Uij restraint ( rigid bond, approximate isotropic, tied
)' #
# [IDB: Do we really need to go into this amount of detail? Someone is sure
# to find another kind of constraint that can be applied. I recommend
that we
# follow CH's last suggestion and redefine U as:
#
# U
# ;Uiso or Uij as constrained to a value determined by neighbouring or
related
# atoms
# ;
#
# STATUS: Open for discussion
#
#######################################
#
# 9. _ATOM_SITES_SOLUTION_*
#
#######################################
#
# COMMENT: Bruce Noll has suggested (2005-02-22) that the enumeration list
# needs updating to include 'other' in addition to at least Sheldrick's Dual
# Space method. This would require the following additions to the
enumeration
# list of _atom_sites_solution_*
loop_ _enumeration _enumeration_detail
dual 'Sheldrick's dual space method (***reference
needed***)'
other 'a method not included elsewhere in this list'
#
# STATUS: Open for discussion
#
#######################################
#
# 10. _CHEMICAL_ENANTIOEXCESS_BULK_*
#
#######################################
#
# HDF (05-07-25) suggests the need for the following item
#
data_chemical_enantioexcess_bulk
_name '_chemical_enantioexcess_bulk'
_category chemical
_type numb
_type_conditions esd
_enumeration_range 0.0:1.0
_units U
# See the note on units in Section D below
_units_detail dimensionless
_definition
; The enantioexcess of the bulk material from which the
crystals were grown.
A value of 0.0 indicates the racemate. A value of 1.0
indicates that the compound is enantiomerically pure.
Enantioexcess is defined in the IUPAC Recommendations
1996, Basic Terminology of Stereochemistry, Moss G.P. (1996)
Pure and Applied Chemistry, 68, 2193-2222, available at
http://www.chem.qmul.ac.uk/iupac/stereo/index.html
;
data_chemical_enantioexcess_bulk_technique
_name '_chemical_enantioexcess_bulk_technique'
_category chemical
_type char
loop_ _enumeration
_enumeration_detail OA
; enantioexcess determined by
measurement of the specific rotation
of the optical activity of the bulk
compound in solution
;
CD
; enantioexcess determined by
measurement of the visible/near UV
circular dichroism spectrum of the
bulk compound in solution
;
EC
; enantioexcess determined by
enantioselective chromatography of
the bulk compound in solution
;
_definition
; The experimental technique used to determine the
enantioexcess of the bulk compound.
;
data_chemical_enantioexcess_crystal
_name '_chemical_enantioexcess_crystal'
_category chemical
_type numb
_type_conditions esd
_enumeration_range 0.0:1.0
_units U
# See the note on units in Section D below
_units_detail dimensionless
_definition
; The enantioexcess of the crystal used for the diffraction
study. A value of 0.0 indicates the racemate. A value of
1.0 indicates that the crystal is enantiomerically pure.
Enantioexcess is defined in the IUPAC Recommendations
1996, Basic Terminology of Stereochemistry, Moss G.P. (1996)
Pure and Applied Chemistry, 68, 2193-2222, available at
http://www.chem.qmul.ac.uk/iupac/stereo/index.html
;
data_chemical_enantioexcess_crystal_technique
_name '_chemical_enantioexcess_crystal_technique'
_category chemical
_type char
loop_ _enumeration
_enumeration_detail CD
; enantioexcess determined by
measurement of the visible/near UV
circular dichroism spectrum of the
crystal taken into solution
;
EC
; enantioexcess determined by
enantioselective chromatography of
the crystal taken into solution
;
_definition
; The experimental technique used to determine the
enantioexcess of the crystal.
;
#
# STATUS: Open for discussion
#
#################################
#
# 11. _PUBL_SECTION_KEYWORDS
#
#################################
#
# Doug Boulay (05-06-25):
# After reading David's report,
# I notice the the current CIF dictionaries
# don't seem to have any explicit publication specific keyword
# metadata definitions, such as
#
# _publ_manuscript_keywords
# or
# _publ_section_keywords
#
# Probably just an oversight considering the wealth of
# other _publ_ and _journal_ definitions therein.
# But it could be quite useful for propagating into
# Dublin-core (RDF) subject metadata for HTML and XML
# renderings of CIF. It would probably need an official vocabulary of
# terms and terminology to do it rigorously though.
#
# mmCIF does have these definitions:
#
# _entity_keywords.text
# _struct_keywords.text
# _struct_biol_keywords.text
# _struct_site_keywords.text
#
# [IDB: These items do not have an enumeration list]
#
data_publ_section_keywords
_name '_publ_section_keywords'
_category publ
_type char
_list yes
_list_reference '_publ_section_keywords_id'
_example ?
_definition
; Keywords associated with the manuscript
;
data_publ_section_keywords_id
_name '_publ_section_keywords_id'
_category publ
_type char
_list yes
_list_mandatory yes
_example ?
_definition
; A unique identifier for a keyword in a list.
;
#
# STATUS: Open for discussion
#
########################
#
# 12. DIMENSIONLESS UNITS
#
# COMMENT: HDF provides the following information
#
# 24.1 Interdivisional Committee on Terminology, Nomenclature and Symbols of
# the International Union of Pure and Applied Chemistry (IUPAC ICTNS)
#
# Another proposal concerns the use of the name 'uno', symbol U, for the
unit
# one so that dimensionless numbers may be treated in the same way as all
# other SI units.
# Thus, a second phase in a material detected at a 15 \mg/kg level, for
# example, would be expressed as 15 nU (15 nanouno) of that phase.
# Among other advantages, the proposed unit eliminates the present
widespread
# and sometimes ambiguous use of abbreviations such as ppm (for the number
# 10^-6^), ppb (for the number 10^-9^ in the USA and UK, 10^-12^ in
# continental Europe).
# CCU had proposed the name uno in 1999 but no action was taken at that time
# by the Comité International des Poids et Mesures.
# All Directors of National Institutes of Metrology and other relevant
# institutions have been canvassed for the widest views on the proposal.
#
# [IDB: adding uno to the list of units would result in the following item.]
#
data_units
_definition
; A unique code which identifies the units of the defined data
item. A description of the units is provided in
_units_detail.
;
_name '_units'
_category units
_type char
loop_ _example
_example_detail K 'kelvins'
C 'degrees Celsius'
rad 'radians'
e 'electrons'
V 'volts'
Dal 'daltons'
m 'metres'
kg 'kilograms'
s 'seconds'
U 'uno (dimensionless units)'
#
# STATUS: Open for discussion
#
################################
################################
#
# D. OTHER OUTSTANDING ITEMS
#
################################
#
# TWINS
#
# Simon Parsons, Vic Young and colleagues are working on a description of
# twinning.
# Their proposal is not yet ready to bring to the DMG.
#
# DETAILS OF SCANS FOR INDIVIDUAL REFLECTIONS
#
# (angles, ranges etc.) Suggested by Curt Haltiwanger.
# They will require a new category diffrn_refln_scan.
# Curt is currently preparing definitions.
#
# TREATMENT OF STANDARD UNCERTAINTY
#
# Some items that occur with standard uncertainties have enumeration ranges
# that are determined by physical limitations.
# For example, an occupation number cannot physically be greater than 1.0 or
# less than zero.
# However, experimentally measured values may be as much as 3*sigma less
than
# zero or 3*sigma greater than 1.0.
# At present there is no way in which information on the correct
# treatment of enumeration ranges for experimentally determined
quantities is
# coded in a machine readable (or any other) form.
# Does anyone have any suggestions?
#
# MACHINE-INDEPENDENT AXES
#
# Ross Angel suggests that in high pressure work it is better to
describe the
# crystal shape in a diffractometer-based Cartesian coordinate system rather
# than a reciprocal-cell based system.
# The conversion between these is related to the orientation matrix of the
# crystal but the present definition of this matrix is unsatisfactory
because
# it depends on the design of the diffractometer.
# Recently a unique definition of a Cartesian coordinate system that
does not
# involve the direction of gravity (up-down) has been prepared for the
imgCIF
# dictionary.
# This should become the standard for all CIFs and should appear
somewhere in
# the core.
#
# The convention is given in the introduction to the AXIS category in imgCIF
# and can be summarized as follows:
#
# The ORIGIN is chosen at the centre of the specimen.
# The X axis is aligned to the principal mechanical axis of the goniometer
# This is the axis of the circle furthest removed from the specimen; it is
# usually fixed in the laboratory space and is frequently vertical or
# horizontal.
# The Y axis is perpendicular to the plane defined by the X axis and the
# incident beam, maintaining a right-handed system with X and Z.
# The Z axis is perpendicular to X and Y and its positive direction is
on the
# same side of the XY plane as the radiation source.
# Any axis system can be defined in terms of these vectors and an origin
# shift vector (in mm) from the specimen.
#
#########################################################
# The following is a template that can be used for new definitions
data_
_name
_category
_type
_type_conditions
_list
_list_reference
_list_mandatory
_related_item
_related_function
_enumeration_range
_units
_units_detail
_example
_definition
;
;
# COMMENT:
# STATUS:
begin:vcard fn:I.David Brown n:Brown;I.David org:McMaster University;Brockhouse Institute for Materials Research adr:;;King St. W;Hamilton;Ontario;L8S 4M1;Canada email;internet:[email protected] title:Professor Emeritus tel;work:+905 525 9140 x 24710 tel;fax:+905 521 2773 version:2.1 end:vcard
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